Variant report

Variant	rs1556935
Chromosome Location	chr1:180475368-180475369
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	STAT3	chr1:180475143-180475408	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:180474982-180475478	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:180475307-180475459	MCF10A-Er-Src	breast:	n/a	n/a
4	E2F4	chr1:180475160-180475518	MCF10A-Er-Src	breast:	n/a	n/a
5	CHD2	chr1:180475243-180475410	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr1:180475324-180475386	Hela-S3	cervix:	n/a	n/a
7	FOS	chr1:180474916-180475480	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
8	STAT3	chr1:180474992-180475538	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:180475024-180475451	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:180474883-180475453	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
11	FOS	chr1:180474852-180475499	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
12	STAT3	chr1:180475102-180475503	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:180475072-180475477	HUVEC	blood vessel:	n/a	chr1:180475268-180475279 chr1:180475270-180475278
14	CEBPB	chr1:180475162-180475436	IMR90	lung:	n/a	n/a
15	STAT3	chr1:180475341-180475537	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr1:180475011-180475478	MCF10A-Er-Src	breast:	n/a	chr1:180475268-180475279 chr1:180475270-180475278

No.	Distal block	Cell Line	Cell type
1	chr1:180462761..180465502-chr1:180475330..180477923,2	K562	blood:
2	chr1:180469977..180474881-chr1:180475033..180479240,11	K562	blood:
3	chr1:180469977..180473874-chr1:180475273..180479240,10	K562	blood:

Variant related genes	Relation type
ACBD6	TF binding region
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10157891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10733005	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10737343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753210	1.00[ASN][1000 genomes]
rs10753213	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753214	1.00[ASN][1000 genomes]
rs10753217	1.00[ASN][1000 genomes]
rs10798744	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798749	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914019	1.00[ASN][1000 genomes]
rs10914020	1.00[ASN][1000 genomes]
rs1094597	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094598	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094599	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027553	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077904	1.00[ASN][1000 genomes]
rs12144149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565152	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339726	1.00[ASN][1000 genomes]
rs1361363	1.00[ASN][1000 genomes]
rs1361628	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556938	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934411	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935283	1.00[ASN][1000 genomes]
rs1961741	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153327	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2153753	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2262371	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2331739	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331742	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2764432	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764434	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764435	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764436	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764437	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764438	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764439	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764440	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764441	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764442	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764444	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764467	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764468	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794969	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794970	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794971	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794972	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794973	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794974	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794975	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794976	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259605	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281291	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333819	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4540612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609392	1.00[ASN][1000 genomes]
rs4651061	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651063	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651066	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4651067	1.00[ASN][1000 genomes]
rs4652501	1.00[ASN][1000 genomes]
rs4652502	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4652506	1.00[ASN][1000 genomes]
rs4652510	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61811598	1.00[AFR][1000 genomes]
rs61811599	1.00[AFR][1000 genomes]
rs61811602	1.00[AFR][1000 genomes]
rs61811603	1.00[AFR][1000 genomes]
rs61811605	1.00[AFR][1000 genomes]
rs61811613	1.00[AFR][1000 genomes]
rs61811614	1.00[AFR][1000 genomes]
rs61811617	1.00[AFR][1000 genomes]
rs61811618	1.00[AFR][1000 genomes]
rs61811619	1.00[AFR][1000 genomes]
rs61811621	1.00[AFR][1000 genomes]
rs61811627	1.00[AFR][1000 genomes]
rs61811628	1.00[AFR][1000 genomes]
rs6425620	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425621	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425622	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425623	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425626	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425647	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659147	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664944	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665615	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667478	1.00[ASN][1000 genomes]
rs6669304	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678261	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6680754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682067	0.91[ASN][1000 genomes]
rs6683484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684842	1.00[ASN][1000 genomes]
rs6687873	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695360	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515052	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522928	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529042	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7530015	0.90[EUR][1000 genomes]
rs7532972	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542568	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543143	1.00[ASN][1000 genomes]
rs7546030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548884	1.00[ASN][1000 genomes]
rs7555087	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822703	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822704	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863720	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863721	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425879	1.00[ASN][1000 genomes]
rs946633	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946634	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946635	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180472400-180477600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:180472400-180481400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:180472600-180477000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180472800-180477200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:180472800-180488800	Weak transcription	Right Atrium	heart
6	chr1:180473000-180476800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:180473000-180476800	Weak transcription	K562	blood
8	chr1:180473000-180477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:180473600-180475800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:180473600-180477000	Weak transcription	HMEC	breast
11	chr1:180474200-180475400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:180474400-180475400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:180474400-180475600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:180474400-180477800	Enhancers	HUVEC	blood vessel
15	chr1:180474800-180475600	Enhancers	Hela-S3	cervix
16	chr1:180474800-180481800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:180475000-180475400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:180475000-180475400	Enhancers	NHDF-Ad	bronchial
19	chr1:180475000-180475400	Flanking Active TSS	Osteobl	bone
20	chr1:180475000-180475600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:180475000-180475600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:180475000-180475800	Enhancers	NHLF	lung
23	chr1:180475200-180475400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:180475200-180475400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:180475200-180475600	Enhancers	A549	lung
26	chr1:180475200-180475600	Enhancers	NH-A	brain

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