Variant report

Variant	rs4950382
Chromosome Location	chr1:146648224-146648225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000131778	Chromatin interaction
ENSG00000131781	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000273071	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs11239954	0.95[CEU][hapmap]
rs11800580	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11811023	0.83[GIH][hapmap];0.96[TSI][hapmap]
rs12046706	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17159924	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17160050	0.95[CEU][hapmap]
rs17160051	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs17355474	0.83[EUR][1000 genomes]
rs17355509	0.90[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs17356184	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs17356219	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17356233	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17356240	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs17359629	0.90[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs17360443	0.95[CEU][hapmap]
rs1822304	0.98[ASN][1000 genomes]
rs1822309	0.84[EUR][1000 genomes]
rs1932977	0.86[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];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1999820	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2077749	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2083720	0.86[EUR][1000 genomes]
rs2354428	0.95[CEU][hapmap]
rs28381210	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2883323	0.95[CEU][hapmap]
rs2883324	0.95[CEU][hapmap]
rs2883434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737855	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs3766519	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs3766520	1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs3766522	0.95[CEU][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4301678	0.95[CEU][hapmap];0.83[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	0.91[EUR][1000 genomes]
rs4950304	0.81[EUR][1000 genomes]
rs4950305	0.81[EUR][1000 genomes]
rs4950306	0.81[EUR][1000 genomes]
rs4950308	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4950313	0.89[EUR][1000 genomes]
rs4950315	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs4950316	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4950318	1.00[CEU][hapmap]
rs4950319	0.85[CEU][hapmap]
rs4950371	0.88[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs4950379	0.92[EUR][1000 genomes]
rs4950384	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4950389	0.91[EUR][1000 genomes]
rs4950392	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs55697094	0.83[EUR][1000 genomes]
rs55799799	0.84[EUR][1000 genomes]
rs56080828	0.97[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	0.95[AMR][1000 genomes];0.88[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];0.85[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	0.91[EUR][1000 genomes]
rs72691012	0.89[EUR][1000 genomes]
rs72691016	0.83[EUR][1000 genomes]
rs72691032	0.83[EUR][1000 genomes]
rs72691033	0.83[EUR][1000 genomes]
rs72691041	0.82[EUR][1000 genomes]
rs72706441	0.86[EUR][1000 genomes]
rs72706444	0.84[EUR][1000 genomes]
rs72708536	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7514970	0.83[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	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541393	0.90[CEU][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap];0.83[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
rs4950382	RP11-337C18.8	cis	Thyroid	GTEx
rs4950382	CHD1L	cis	Whole Blood	GTEx
rs4950382	PRKAB2	cis	cerebellum	SCAN
rs4950382	CHD1L	cis	cerebellum	SCAN

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	chr1:146645400-146649000	Weak transcription	HSMM	muscle
5	chr1:146645400-146649600	Weak transcription	Aorta	Aorta
6	chr1:146645400-146649600	Weak transcription	Ovary	ovary
7	chr1:146645400-146649600	Weak transcription	Thymus	Thymus
8	chr1:146645400-146664400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:146645400-146674800	Weak transcription	Gastric	stomach
10	chr1:146645600-146649200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:146645600-146649400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:146645600-146649400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:146645600-146649400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:146645600-146649400	Weak transcription	Psoas Muscle	Psoas
15	chr1:146645600-146649400	Weak transcription	HMEC	breast
16	chr1:146645600-146649600	Weak transcription	Pancreas	Pancrea
17	chr1:146645600-146649600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:146645600-146649600	Weak transcription	Spleen	Spleen
19	chr1:146645600-146649800	Weak transcription	Fetal Lung	lung
20	chr1:146645600-146650200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:146645600-146651800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:146645600-146661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:146645800-146648400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:146645800-146648600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:146645800-146648800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:146645800-146649000	Weak transcription	NHDF-Ad	bronchial
27	chr1:146645800-146649600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:146645800-146649800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:146645800-146649800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:146645800-146675200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:146646000-146649000	Weak transcription	NHEK	skin
32	chr1:146646000-146649200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:146646000-146649200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:146646000-146649400	Weak transcription	Fetal Kidney	kidney
35	chr1:146646000-146649400	Weak transcription	HUVEC	blood vessel
36	chr1:146646000-146649400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:146646000-146649600	Weak transcription	Liver	Liver
38	chr1:146646000-146649600	Weak transcription	Left Ventricle	heart
39	chr1:146646000-146650200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:146646000-146651600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:146646000-146655400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:146646000-146656000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:146646000-146661200	Weak transcription	Brain Angular Gyrus	brain
44	chr1:146646200-146648600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:146646200-146649000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:146646200-146649000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:146646200-146649000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:146646200-146649000	Weak transcription	NHLF	lung
49	chr1:146646200-146649000	Weak transcription	Osteobl	bone
50	chr1:146646200-146649200	Weak transcription	Colon Smooth Muscle	Colon

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