Variant report

Variant	rs1470261
Chromosome Location	chr1:146694922-146694923
allele	C/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	POLR2A	chr1:146694728-146694954	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:146693138-146696033	HepG2	liver:	n/a	n/a
3	HEY1	chr1:146693921-146696141	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:146693731-146696042	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146644917..146647495-chr1:146694467..146696944,2	K562	blood:
2	chr1:146642791..146647744-chr1:146694916..146698486,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236806	TF binding region
ENSG00000273071	Chromatin interaction
ENSG00000271721	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000237188	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1036850	0.86[EUR][1000 genomes]
rs1036851	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs10900321	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1123333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11239953	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs11239955	0.87[ASN][1000 genomes]
rs11239956	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs12029358	0.80[CHB][hapmap]
rs12093458	0.87[ASN][1000 genomes]
rs12736102	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs1348316	0.84[MEX][hapmap]
rs1470262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932978	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs2078325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083719	0.80[AMR][1000 genomes]
rs4950391	0.87[ASN][1000 genomes]
rs6593739	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6593750	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs6593752	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs6670503	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704497	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517655	0.84[AMR][1000 genomes]
rs7519804	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs7548820	0.81[ASN][1000 genomes]
rs930495	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 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
25	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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	44 gene(s)	inside rSNPs	diseases
26	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
27	nsv872258	chr1:146662018-146709784	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
28	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
29	nsv872259	chr1:146688941-146724923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1470261	CHD1L	cis	cerebellum	SCAN
rs1470261	ACP6	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146649800-146695400	Weak transcription	Left Ventricle	heart
2	chr1:146658800-146695400	Weak transcription	Lung	lung
3	chr1:146659000-146695200	Weak transcription	Ovary	ovary
4	chr1:146672800-146696400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:146674200-146696600	Weak transcription	Brain Anterior Caudate	brain
6	chr1:146674400-146695400	Weak transcription	Right Ventricle	heart
7	chr1:146675000-146695000	Weak transcription	Fetal Stomach	stomach
8	chr1:146676800-146696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:146678400-146696200	Weak transcription	Colonic Mucosa	Colon
10	chr1:146679800-146696600	Weak transcription	Primary T cells from cord blood	blood
11	chr1:146680600-146696400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:146681200-146696400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:146681800-146696400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:146682800-146695400	Weak transcription	Spleen	Spleen
15	chr1:146683800-146696400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:146684000-146695400	Weak transcription	Small Intestine	intestine
17	chr1:146684000-146696400	Weak transcription	Adipose Nuclei	Adipose
18	chr1:146685200-146696600	Weak transcription	Aorta	Aorta
19	chr1:146685400-146695200	Weak transcription	Pancreas	Pancrea
20	chr1:146686000-146695200	Weak transcription	Gastric	stomach
21	chr1:146686600-146696400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:146687000-146695600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:146687200-146696400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:146687200-146696400	Weak transcription	Fetal Intestine Large	intestine
25	chr1:146687400-146696400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:146687600-146695400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:146688000-146695200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:146688000-146696400	Weak transcription	Fetal Intestine Small	intestine
29	chr1:146688400-146695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:146688400-146695400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:146690800-146696400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:146691200-146695400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:146692200-146696400	Weak transcription	Fetal Kidney	kidney
34	chr1:146693600-146695600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:146694000-146695000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:146694400-146695400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:146694400-146695800	Flanking Active TSS	Liver	Liver
38	chr1:146694400-146695800	Enhancers	Brain Substantia Nigra	brain
39	chr1:146694800-146695200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:146694800-146695200	Transcr. at gene 5' and 3'	HepG2	liver
41	chr1:146694800-146695400	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:146694800-146695600	Flanking Active TSS	Stomach Mucosa	stomach
43	chr1:146694800-146696000	Enhancers	Fetal Lung	lung
44	chr1:146694800-146696400	Weak transcription	Brain Angular Gyrus	brain

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