Variant report

Variant	rs3007708
Chromosome Location	chr1:151967836-151967837
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	RCOR1	chr1:151967470-151967868	Hela-S3	cervix:	n/a	n/a
2	FOS	chr1:151967386-151967892	MCF10A-Er-Src	breast:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
3	REST	chr1:151967329-151968134	PANC-1	pancreas:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
4	BCL3	chr1:151967331-151967984	A549	lung:	n/a	n/a
5	TEAD4	chr1:151967261-151967961	SK-N-SH	brain:	n/a	n/a
6	STAT3	chr1:151967357-151967894	MCF10A-Er-Src	breast:	n/a	chr1:151967656-151967667 chr1:151967452-151967464
7	POLR2A	chr1:151967398-151967942	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr1:151963929-151968128	A549	lung:	n/a	chr1:151964984-151964991
9	CEBPB	chr1:151967515-151967926	A549	lung:	n/a	n/a
10	POLR2A	chr1:151967298-151968152	PANC-1	pancreas:	n/a	n/a
11	SIN3AK20	chr1:151967329-151967838	PANC-1	pancreas:	n/a	n/a
12	REST	chr1:151967432-151967948	HL-60	blood:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
13	ATF3	chr1:151967347-151967909	A549	lung:	n/a	n/a
14	BCL3	chr1:151967315-151967962	A549	lung:	n/a	n/a
15	REST	chr1:151967507-151967845	H1-hESC	embryonic stem cell:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
16	MAFK	chr1:151967466-151967878	Hela-S3	cervix:	n/a	chr1:151967709-151967723
17	BRCA1	chr1:151967469-151967859	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr1:151967494-151967963	Hela-S3	cervix:	n/a	chr1:151967656-151967671 chr1:151967654-151967669
19	FOSL1	chr1:151967270-151968006	HCT-116	colon:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
20	JUND	chr1:151967265-151967944	SK-N-SH	brain:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
21	RAD21	chr1:151967417-151967884	A549	lung:	n/a	n/a
22	FOSL2	chr1:151967326-151968033	SK-N-SH	brain:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
23	POLR2A	chr1:151967325-151967839	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr1:151960197-151968028	U87	brain:	n/a	n/a
25	JUND	chr1:151967366-151967851	A549	lung:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
26	POLR2A	chr1:151967416-151967900	Hela-S3	cervix:	n/a	n/a
27	REST	chr1:151967449-151967872	SK-N-SH	brain:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
28	EP300	chr1:151967321-151968049	A549	lung:	n/a	n/a
29	SIN3AK20	chr1:151967355-151967955	A549	lung:	n/a	n/a
30	EP300	chr1:151967367-151967992	SK-N-SH	brain:	n/a	n/a
31	TCF12	chr1:151967297-151967865	A549	lung:	n/a	n/a
32	SIX5	chr1:151967203-151967982	A549	lung:	n/a	n/a
33	PBX3	chr1:151967307-151967922	SK-N-SH	brain:	n/a	n/a
34	NR3C1	chr1:151967444-151967845	A549	lung:	n/a	n/a
35	MAX	chr1:151967275-151967928	A549	lung:	n/a	chr1:151967456-151967466
36	ZKSCAN1	chr1:151967518-151967877	Hela-S3	cervix:	n/a	n/a
37	FOSL2	chr1:151967245-151968199	A549	lung:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
38	STAT3	chr1:151967416-151968681	MCF10A-Er-Src	breast:	n/a	chr1:151967656-151967667 chr1:151967452-151967464
39	CEBPB	chr1:151967294-151968021	A549	lung:	n/a	n/a
40	REST	chr1:151967375-151968025	Hela-S3	cervix:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
41	REST	chr1:151967304-151968171	A549	lung:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
42	SMARCC1	chr1:151967352-151967978	Hela-S3	cervix:	n/a	chr1:151967483-151967492
43	REST	chr1:151967347-151967963	ECC-1	luminal epithelium:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
44	SMC3	chr1:151967413-151967865	Hela-S3	cervix:	n/a	n/a
45	REST	chr1:151967513-151967904	U87	brain:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
46	REST	chr1:151967394-151968075	A549	lung:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
47	JUND	chr1:151967296-151967928	SK-N-SH	brain:	n/a	chr1:151967485-151967496 chr1:151967484-151967492 chr1:151967458-151967467
48	REST	chr1:151967471-151967992	ECC-1	luminal epithelium:	n/a	chr1:151967704-151967714 chr1:151967726-151967735 chr1:151967702-151967716
49	GABPA	chr1:151967320-151967914	A549	lung:	n/a	chr1:151967457-151967466
50	TEAD4	chr1:151967288-151967880	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:
2	chr1:151879131..151885542-chr1:151961269..151968730,13	MCF-7	breast:
3	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
4	chr1:151906249..151906867-chr1:151967800..151968301,2	MCF-7	breast:
5	chr1:151880209..151887387-chr1:151961986..151968084,15	MCF-7	breast:

Variant related genes	Relation type
S100A10	TF binding region
ENSG00000159445	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1038747	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10494270	0.81[CHB][hapmap]
rs10788817	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10788820	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11204915	0.81[CHB][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs11204922	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11542015	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11589720	0.85[ASN][1000 genomes]
rs12083193	0.95[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs12116923	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13320	0.86[MEX][hapmap]
rs1387833	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1532133	0.91[CHB][hapmap]
rs16833668	0.86[CHB][hapmap]
rs16833728	0.91[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs16833743	0.95[CHB][hapmap]
rs1979637	0.85[CHB][hapmap]
rs2279501	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2279502	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs2337689	0.81[ASN][1000 genomes]
rs2338019	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932570	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2932574	0.86[ASN][1000 genomes]
rs2932579	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs2932581	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932583	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932586	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932590	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999508	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999512	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999526	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999528	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999534	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999539	0.83[ASW][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2999542	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2999544	0.81[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs2999560	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2999561	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3007670	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs3007685	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3007691	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3007711	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3791153	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs6587635	0.91[CHB][hapmap]
rs6587636	0.91[CHB][hapmap]
rs6587637	0.84[CHB][hapmap]
rs6587638	0.90[CHB][hapmap]
rs6587640	0.95[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap]
rs6662611	0.91[CHB][hapmap]
rs6663064	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs6678672	0.95[CHB][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs6685187	0.85[MEX][hapmap]
rs6686874	0.86[CHB][hapmap];0.81[TSI][hapmap]
rs6703465	0.91[CHB][hapmap]
rs7535002	0.86[CHB][hapmap]
rs7541099	0.91[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs902313	0.91[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs971887	0.91[CHB][hapmap];0.80[GIH][hapmap];0.87[TSI][hapmap]
rs9943221	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs9943251	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3007708	THEM4	cis	Esophagus Muscularis	GTEx
rs3007708	S100A10	cis	lymphoblastoid	seeQTL
rs3007708	S100A10	cis	cerebellum	SCAN
rs3007708	THEM4	cis	lymphoblastoid	seeQTL
rs3007708	THEM4	cis	uninvolved skin	skin_eQTL
rs3007708	S100A10	cis	Lymphoblastoid	GTEx
rs3007708	SCNM1	cis	parietal	SCAN
rs3007708	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs3007708	THEM4	cis	cerebellum	SCAN
rs3007708	THEM4	cis	multi-tissue	Pritchard
rs3007708	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs3007708	S100A10	cis	multi-tissue	Pritchard
rs3007708	THEM4	cis	Nerve Tibial	GTEx
rs3007708	THEM4	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151966400-151968000	Enhancers	Spleen	Spleen
2	chr1:151966800-151968000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr1:151966800-151968200	Enhancers	HSMMtube	muscle
4	chr1:151966800-151976800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:151967000-151968000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:151967000-151968000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:151967000-151968000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:151967000-151968000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:151967000-151968000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:151967000-151968000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:151967000-151968000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:151967000-151968000	Enhancers	Left Ventricle	heart
13	chr1:151967000-151968000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:151967000-151968000	Enhancers	Stomach Smooth Muscle	stomach
15	chr1:151967000-151968000	Enhancers	HUVEC	blood vessel
16	chr1:151967000-151968800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:151967000-151968800	Enhancers	NHLF	lung
18	chr1:151967000-151969800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:151967000-151970200	Weak transcription	Right Atrium	heart
20	chr1:151967000-151970600	Weak transcription	Esophagus	oesophagus
21	chr1:151967000-151973000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:151967000-151977000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:151967200-151968000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:151967200-151968000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr1:151967200-151968000	Enhancers	Adipose Nuclei	Adipose
26	chr1:151967200-151968200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:151967200-151968200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:151967200-151968200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:151967200-151968200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:151967200-151968200	Enhancers	HepG2	liver
31	chr1:151967200-151968200	Enhancers	NH-A	brain
32	chr1:151967200-151968200	Enhancers	Osteobl	bone
33	chr1:151967200-151968400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:151967200-151968400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:151967200-151968600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:151967200-151968600	Enhancers	HSMM	muscle
37	chr1:151967200-151968800	Enhancers	Fetal Intestine Small	intestine
38	chr1:151967200-151968800	Enhancers	NHDF-Ad	bronchial
39	chr1:151967200-151969200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:151967200-151969400	Enhancers	Fetal Intestine Large	intestine
41	chr1:151967200-151969800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr1:151967200-151970200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:151967200-151973200	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:151967200-151974000	Enhancers	HMEC	breast
45	chr1:151967200-151977000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:151967400-151968000	Enhancers	H9 Cell Line	embryonic stem cell
47	chr1:151967400-151968000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:151967400-151968000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:151967400-151968200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:151967600-151968000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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