Variant report

Variant	rs6684137
Chromosome Location	chr1:95538915-95538916
allele	A/G
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	NR2F2	chr1:95537902-95539266	K562	blood:	n/a	chr1:95538494-95538509
2	MTA3	chr1:95538079-95539206	GM12878	blood:	n/a	n/a
3	EGR1	chr1:95538727-95538929	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:95537954-95539075	GM12878	blood:	n/a	n/a
5	NRF1	chr1:95538200-95539002	GM12878	blood:	n/a	chr1:95538465-95538474 chr1:95538792-95538803 chr1:95538465-95538476
6	MAX	chr1:95537991-95538995	ECC-1	luminal epithelium:	n/a	n/a
7	HEY1	chr1:95538301-95538979	K562	blood:	n/a	n/a
8	ZNF263	chr1:95538268-95538982	HEK293-T-REx	kidney:	n/a	n/a
9	POLR2A	chr1:95538087-95538976	MCF-7	breast:	n/a	n/a
10	RCOR1	chr1:95538033-95538974	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr1:95537860-95539164	GM12878	blood:	n/a	n/a
12	PAX5	chr1:95538642-95538937	GM12878	blood:	n/a	chr1:95538798-95538816
13	POLR2A	chr1:95537770-95539033	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:95537944-95539004	H1-neurons	neurons:	n/a	n/a
15	EGR1	chr1:95538326-95539025	K562	blood:	n/a	chr1:95538466-95538475
16	ELF1	chr1:95537979-95538917	SK-N-SH	brain:	n/a	chr1:95538479-95538488 chr1:95538478-95538489
17	POLR2A	chr1:95538032-95539018	HL-60	blood:	n/a	n/a
18	ARID3A	chr1:95537686-95538981	HepG2	liver:	n/a	n/a
19	MAX	chr1:95537919-95538962	Hela-S3	cervix:	n/a	n/a
20	MYC	chr1:95537993-95539193	K562	blood:	n/a	n/a
21	MAX	chr1:95538086-95538997	K562	blood:	n/a	n/a
22	STAT3	chr1:95537336-95539367	GM12878	blood:	n/a	chr1:95537563-95537570
23	WRNIP1	chr1:95537722-95539035	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:95537633-95539115	PBDE	blood:	n/a	n/a
25	POLR2A	chr1:95538032-95539043	K562	blood:	n/a	n/a
26	POLR2A	chr1:95537781-95539224	SK-N-MC	brain:	n/a	n/a
27	MAX	chr1:95538012-95539035	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr1:95537993-95539044	Hela-S3	cervix:	n/a	n/a
29	GABPA	chr1:95537926-95539054	SK-N-SH	brain:	n/a	chr1:95538465-95538474 chr1:95538465-95538476
30	POLR2A	chr1:95537439-95539039	MCF10A-Er-Src	breast:	n/a	n/a
31	MAZ	chr1:95537997-95539065	K562	blood:	n/a	n/a
32	MAX	chr1:95538121-95538935	K562	blood:	n/a	n/a
33	CBX3	chr1:95538006-95539031	K562	blood:	n/a	n/a
34	TCF12	chr1:95537924-95539031	A549	lung:	n/a	n/a
35	CHD2	chr1:95538032-95539040	GM12878	blood:	n/a	n/a
36	HEY1	chr1:95538270-95538990	HepG2	liver:	n/a	n/a
37	CREB1	chr1:95537957-95539027	GM12878	blood:	n/a	n/a
38	RCOR1	chr1:95538008-95539222	K562	blood:	n/a	n/a
39	BHLHE40	chr1:95537683-95539148	K562	blood:	n/a	n/a
40	POLR2A	chr1:95538053-95539158	HCT-116	colon:	n/a	n/a
41	PML	chr1:95537818-95539195	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:95538059-95539030	K562	blood:	n/a	n/a
43	MXI1	chr1:95537476-95539172	IMR90	lung:	n/a	n/a
44	POLR2A	chr1:95537970-95539030	PFSK-1	brain:	n/a	n/a
45	TBL1XR1	chr1:95538018-95539217	K562	blood:	n/a	n/a
46	ZNF143	chr1:95537930-95538967	K562	blood:	n/a	chr1:95538197-95538206 chr1:95538261-95538279 chr1:95538197-95538215
47	ZNF384	chr1:95537894-95539080	GM12878	blood:	n/a	n/a
48	MAX	chr1:95537834-95538986	NB4	blood:	n/a	chr1:95537844-95537851
49	POLR2A	chr1:95538007-95538960	ECC-1	luminal epithelium:	n/a	n/a
50	MXI1	chr1:95537648-95538927	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:95537299..95540042-chr1:95699496..95701047,2	K562	blood:
2	chr1:95536810..95539827-chr1:95698878..95701315,3	K562	blood:
3	chr1:95538593..95540251-chr1:95544538..95546428,2	K562	blood:

Variant related genes	Relation type
ALG14	TF binding region
ENSG00000226026	Chromatin interaction
ENSG00000122481	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10465759	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165297	0.93[JPT][hapmap];0.83[AMR][1000 genomes]
rs11590106	0.93[JPT][hapmap]
rs11801110	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12129041	0.87[JPT][hapmap]
rs12239887	0.97[ASN][1000 genomes]
rs12751633	0.93[JPT][hapmap]
rs12755096	0.93[JPT][hapmap]
rs12760863	0.93[JPT][hapmap]
rs17112857	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2391390	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34726676	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34850224	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34923964	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35578830	0.98[ASN][1000 genomes]
rs3890785	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4131811	0.93[JPT][hapmap]
rs4300274	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4387224	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540701	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615892	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55902261	0.94[ASN][1000 genomes]
rs55911502	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60846886	0.94[ASN][1000 genomes]
rs6662345	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6671842	0.83[AMR][1000 genomes]
rs6672635	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6674467	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674604	0.93[JPT][hapmap]
rs6678809	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679106	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6680551	1.00[CEU][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap]
rs6687351	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6689195	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6697256	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs6698894	0.83[AMR][1000 genomes]
rs6704022	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71654403	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71654404	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71654405	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71654406	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71654407	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71654408	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7417186	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540821	0.93[JPT][hapmap]
rs859040	0.85[CEU][hapmap]
rs864553	0.85[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95537200-95539000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:95537200-95539200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:95537200-95539200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:95537200-95539200	Active TSS	Colon Smooth Muscle	Colon
5	chr1:95537200-95539200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:95537400-95539000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:95537400-95539000	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr1:95537400-95539000	Active TSS	Brain Germinal Matrix	brain
9	chr1:95537400-95539000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:95537400-95539000	Active TSS	Right Atrium	heart
11	chr1:95537400-95539000	Active TSS	Small Intestine	intestine
12	chr1:95537400-95539000	Active TSS	Stomach Mucosa	stomach
13	chr1:95537400-95539200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:95537400-95539200	Active TSS	Fetal Muscle Trunk	muscle
15	chr1:95537400-95539200	Active TSS	Psoas Muscle	Psoas
16	chr1:95537400-95539400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:95537600-95539000	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:95537600-95539000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:95537600-95539000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:95537600-95539000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:95537600-95539000	ZNF genes & repeats	Fetal Brain Male	brain
22	chr1:95537600-95539000	Active TSS	Fetal Intestine Large	intestine
23	chr1:95537600-95539000	Active TSS	Placenta	Placenta
24	chr1:95537600-95539000	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr1:95537600-95539000	Active TSS	Thymus	Thymus
26	chr1:95537600-95539000	Active TSS	HSMM	muscle
27	chr1:95537600-95539200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:95537600-95539200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr1:95537600-95539200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:95537600-95539200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:95537600-95539200	Active TSS	Aorta	Aorta
32	chr1:95537600-95539200	Active TSS	Brain Substantia Nigra	brain
33	chr1:95537600-95539200	Active TSS	Colonic Mucosa	Colon
34	chr1:95537600-95539200	Active TSS	Fetal Intestine Small	intestine
35	chr1:95537600-95539200	Active TSS	Ovary	ovary
36	chr1:95537600-95539200	Active TSS	Right Ventricle	heart
37	chr1:95537600-95539400	Active TSS	H1 Cell Line	embryonic stem cell
38	chr1:95537600-95539400	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr1:95537600-95539400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr1:95537800-95539000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:95537800-95539000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:95537800-95539000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:95537800-95539000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:95537800-95539000	Active TSS	Brain Hippocampus Middle	brain
45	chr1:95537800-95539000	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr1:95537800-95539000	Active TSS	Fetal Lung	lung
47	chr1:95537800-95539000	Active TSS	Lung	lung
48	chr1:95537800-95539000	Active TSS	K562	blood
49	chr1:95537800-95539000	Active TSS	NHDF-Ad	bronchial
50	chr1:95537800-95539000	Active TSS	NHLF	lung

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