Variant report

Variant	rs2883434
Chromosome Location	chr1:146649084-146649085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:146649067-146649536	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146643914..146646467-chr1:146647158..146650203,5	MCF-7	breast:
2	chr1:146637222..146651713-chr1:146712141..146718911,44	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1L-1	chr1:146647181-146649319	ENSG00000271721.1

Variant related genes	Relation type
PRKAB2	TF binding region
PDIA3P1	TF binding region
ENSG00000131781	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000131778	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11239954	0.95[CEU][hapmap]
rs11800580	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11811023	0.83[GIH][hapmap];0.96[TSI][hapmap]
rs12046706	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12144722	0.94[ASN][1000 genomes]
rs1372820	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17159914	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17159924	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17160050	0.95[CEU][hapmap]
rs17160051	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs17355474	0.82[EUR][1000 genomes]
rs17355509	0.90[CEU][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs17356184	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17356219	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs17356233	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs17356240	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17359629	0.90[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs17360443	0.95[CEU][hapmap]
rs1822304	0.98[ASN][1000 genomes]
rs1822309	0.84[EUR][1000 genomes]
rs1932977	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1999820	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2077749	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2083720	0.85[EUR][1000 genomes]
rs2354428	0.95[CEU][hapmap]
rs28381210	0.98[EUR][1000 genomes]
rs2883323	0.95[CEU][hapmap]
rs2883324	0.95[CEU][hapmap]
rs3737855	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3766519	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs3766520	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs3766522	0.95[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4301678	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs4373796	0.94[CEU][hapmap]
rs4453096	0.95[CEU][hapmap]
rs4558036	0.90[ASN][1000 genomes]
rs4568882	0.95[CEU][hapmap]
rs4593887	0.90[EUR][1000 genomes]
rs4950304	0.81[EUR][1000 genomes]
rs4950305	0.81[EUR][1000 genomes]
rs4950308	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs4950313	0.88[EUR][1000 genomes]
rs4950315	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4950316	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs4950318	1.00[CEU][hapmap]
rs4950319	0.85[CEU][hapmap]
rs4950371	0.88[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4950379	0.91[EUR][1000 genomes]
rs4950382	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950384	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4950389	0.90[EUR][1000 genomes]
rs4950392	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs55697094	0.82[EUR][1000 genomes]
rs55799799	0.84[EUR][1000 genomes]
rs56080828	0.96[EUR][1000 genomes]
rs56151278	0.81[EUR][1000 genomes]
rs56198825	0.81[EUR][1000 genomes]
rs61838951	0.81[EUR][1000 genomes]
rs6593745	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6593749	0.83[JPT][hapmap]
rs6660507	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686480	0.90[CEU][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap]
rs6703892	0.95[CEU][hapmap]
rs718369	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs720609	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs72691004	0.90[EUR][1000 genomes]
rs72691012	0.88[EUR][1000 genomes]
rs72691016	0.82[EUR][1000 genomes]
rs72691032	0.82[EUR][1000 genomes]
rs72691033	0.82[EUR][1000 genomes]
rs72691041	0.81[EUR][1000 genomes]
rs72706441	0.85[EUR][1000 genomes]
rs72706444	0.84[EUR][1000 genomes]
rs72708536	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7514970	0.82[EUR][1000 genomes]
rs7515160	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7523021	0.92[ASN][1000 genomes]
rs7525703	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7527894	0.92[ASN][1000 genomes]
rs7538682	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541393	0.90[CEU][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs7548475	0.97[ASN][1000 genomes]
rs7554833	0.95[CEU][hapmap]
rs972368	0.90[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
4	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
7	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
8	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
10	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
15	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
16	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
21	nsv872257	chr1:146643555-146724923	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
23	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2883434	PRKAB2	cis	cerebellum	SCAN
rs2883434	RP11-337C18.8	cis	Thyroid	GTEx
rs2883434	CHD1L	cis	cerebellum	SCAN
rs2883434	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146645000-146649600	Weak transcription	Esophagus	oesophagus
2	chr1:146645000-146649600	Weak transcription	Lung	lung
3	chr1:146645200-146649800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:146645400-146649600	Weak transcription	Aorta	Aorta
5	chr1:146645400-146649600	Weak transcription	Ovary	ovary
6	chr1:146645400-146649600	Weak transcription	Thymus	Thymus
7	chr1:146645400-146664400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:146645400-146674800	Weak transcription	Gastric	stomach
9	chr1:146645600-146649200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:146645600-146649400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:146645600-146649400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:146645600-146649400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:146645600-146649400	Weak transcription	Psoas Muscle	Psoas
14	chr1:146645600-146649400	Weak transcription	HMEC	breast
15	chr1:146645600-146649600	Weak transcription	Pancreas	Pancrea
16	chr1:146645600-146649600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:146645600-146649600	Weak transcription	Spleen	Spleen
18	chr1:146645600-146649800	Weak transcription	Fetal Lung	lung
19	chr1:146645600-146650200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:146645600-146651800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:146645600-146661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:146645800-146649600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:146645800-146649800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:146645800-146649800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:146645800-146675200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:146646000-146649200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:146646000-146649200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:146646000-146649400	Weak transcription	Fetal Kidney	kidney
29	chr1:146646000-146649400	Weak transcription	HUVEC	blood vessel
30	chr1:146646000-146649400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:146646000-146649600	Weak transcription	Liver	Liver
32	chr1:146646000-146649600	Weak transcription	Left Ventricle	heart
33	chr1:146646000-146650200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:146646000-146651600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:146646000-146655400	Weak transcription	Brain Anterior Caudate	brain
36	chr1:146646000-146656000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:146646000-146661200	Weak transcription	Brain Angular Gyrus	brain
38	chr1:146646200-146649200	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:146646200-146649200	Weak transcription	Fetal Heart	heart
40	chr1:146646200-146649200	Weak transcription	HSMMtube	muscle
41	chr1:146646200-146649200	Weak transcription	NH-A	brain
42	chr1:146646200-146649600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:146646200-146649600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:146646200-146651200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:146646200-146657000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:146646400-146649200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:146646600-146649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:146646600-146649200	Weak transcription	Small Intestine	intestine
49	chr1:146646600-146649400	Weak transcription	Adipose Nuclei	Adipose
50	chr1:146646600-146649600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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