Variant report

Variant	rs6676502
Chromosome Location	chr1:84972277-84972278
allele	C/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	E2F1	chr1:84971324-84972485	Hela-S3	cervix:	n/a	chr1:84971926-84971935 chr1:84972198-84972208 chr1:84971524-84971534
2	EP300	chr1:84972027-84972929	GM12878	blood:	n/a	n/a
3	HEY1	chr1:84971643-84972670	HepG2	liver:	n/a	n/a
4	MAZ	chr1:84971137-84972836	IMR90	lung:	n/a	n/a
5	IKZF1	chr1:84972005-84972412	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:84971238-84972593	GM12892	blood:	n/a	n/a
7	EBF1	chr1:84972105-84972542	GM12878	blood:	n/a	n/a
8	REST	chr1:84972062-84972506	SK-N-SH	brain:	n/a	n/a
9	TBP	chr1:84971283-84972881	K562	blood:	n/a	n/a
10	JUN	chr1:84970079-84973077	K562	blood:	n/a	chr1:84970176-84970185 chr1:84972305-84972317 chr1:84972307-84972316
11	NRF1	chr1:84971064-84972823	SK-N-SH	brain:	n/a	chr1:84971351-84971360 chr1:84971927-84971936 chr1:84971925-84971936 chr1:84971924-84971935 chr1:84971925-84971939 chr1:84971922-84971936 chr1:84971925-84971934
12	CEBPB	chr1:84972171-84972730	K562	blood:	n/a	n/a
13	SPI1	chr1:84971841-84972534	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:84971217-84972772	GM15510	blood:	n/a	n/a
15	HEY1	chr1:84971631-84972609	HepG2	liver:	n/a	n/a
16	CUX1	chr1:84971961-84973147	K562	blood:	n/a	n/a
17	ATF1	chr1:84972132-84972734	K562	blood:	n/a	n/a
18	BCLAF1	chr1:84972010-84972831	K562	blood:	n/a	chr1:84972323-84972332
19	POLR2A	chr1:84969985-84972746	HCT-116	colon:	n/a	n/a
20	MXI1	chr1:84970410-84973047	GM12878	blood:	n/a	n/a
21	SP1	chr1:84971764-84972647	A549	lung:	n/a	chr1:84972323-84972332 chr1:84972324-84972333 chr1:84972322-84972334 chr1:84972322-84972334
22	POLR2A	chr1:84971534-84972304	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr1:84970990-84972853	K562	blood:	n/a	n/a
24	CTCF	chr1:84971741-84972579	K562	blood:	n/a	n/a
25	EP300	chr1:84971831-84972535	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:84971229-84972553	Gliobla	brain:	n/a	n/a
27	STAT5A	chr1:84971949-84972676	GM12878	blood:	n/a	chr1:84972319-84972331
28	IRF1	chr1:84971421-84972695	K562	blood:	n/a	chr1:84972218-84972230 chr1:84972255-84972264
29	ZNF263	chr1:84971046-84972448	HEK293-T-REx	kidney:	n/a	chr1:84971986-84972007
30	POLR2A	chr1:84970863-84972828	GM18526	blood:	n/a	n/a
31	YY1	chr1:84971271-84972527	HepG2	liver:	n/a	chr1:84972321-84972332
32	MYC	chr1:84972271-84972386	GM12878	blood:	n/a	n/a
33	ATF3	chr1:84972161-84972439	K562	blood:	n/a	chr1:84972324-84972333
34	TAF1	chr1:84971197-84972633	H1-hESC	embryonic stem cell:	n/a	n/a
35	EP300	chr1:84971774-84972530	HepG2	liver:	n/a	n/a
36	EGR1	chr1:84971402-84972613	K562	blood:	n/a	chr1:84971989-84972003 chr1:84972320-84972329 chr1:84972319-84972332 chr1:84971926-84971935
37	POLR2A	chr1:84970891-84972710	PFSK-1	brain:	n/a	n/a
38	MAFK	chr1:84971826-84972477	IMR90	lung:	n/a	chr1:84972251-84972266
39	MAX	chr1:84970764-84972587	Hela-S3	cervix:	n/a	n/a
40	HDAC2	chr1:84971483-84972519	HepG2	liver:	n/a	chr1:84971927-84971936
41	POLR2A	chr1:84971177-84972602	U87	brain:	n/a	n/a
42	TAF1	chr1:84971875-84972526	GM12892	blood:	n/a	n/a
43	YY1	chr1:84971233-84972635	GM12878	blood:	n/a	chr1:84972321-84972332
44	POLR2A	chr1:84970344-84972750	GM12892	blood:	n/a	n/a
45	FOSL1	chr1:84971962-84972478	K562	blood:	n/a	chr1:84972305-84972316 chr1:84972305-84972317 chr1:84972307-84972316
46	POLR2A	chr1:84970407-84973119	GM19099	blood:	n/a	n/a
47	KAP1	chr1:84971879-84972539	HEK293	kidney:	n/a	n/a
48	ZC3H11A	chr1:84972035-84972678	K562	blood:	n/a	n/a
49	POLR2A	chr1:84971357-84972460	MCF-7	breast:	n/a	n/a
50	SIN3AK20	chr1:84971113-84972804	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84971995..84972650-chrX:12993058..12993639,2	Hela-S3	cervix:
2	chr1:84971976..84972761-chr19:2475858..2476389,2	Hela-S3	cervix:
3	chr1:84971986..84972524-chr17:8076562..8077156,2	Hela-S3	cervix:
4	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
5	chr1:84971759..84972422-chr18:12883583..12884223,2	Hela-S3	cervix:
6	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
7	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
8	chr1:84972229..84973001-chr12:6798534..6799186,2	Hela-S3	cervix:
9	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
10	chr1:84971619..84972363-chr2:85765880..85766611,2	HCT-116	colon:
11	chr1:84969596..84972494-chr1:85154864..85156849,3	K562	blood:
12	chr1:84971286..84972368-chr15:75659986..75660965,3	Hela-S3	cervix:
13	chr1:84970994..84973830-chr1:85154472..85157447,5	K562	blood:
14	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
15	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:

Variant related genes	Relation type
GNG5	TF binding region
ENSG00000175354	Chromatin interaction
ENSG00000205542	Chromatin interaction
ENSG00000142875	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000126746	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000271576	Chromatin interaction
ENSG00000099860	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10493754	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10874449	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163973	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11163974	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163975	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11163976	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11163982	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11163985	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11163986	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11163987	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11163993	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164001	0.81[ASN][1000 genomes]
rs12075532	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12354394	0.81[ASN][1000 genomes]
rs13093	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17110164	0.96[ASN][1000 genomes]
rs17110485	0.96[ASN][1000 genomes]
rs17110590	0.96[ASN][1000 genomes]
rs17110949	0.81[ASN][1000 genomes]
rs3768247	0.81[ASN][1000 genomes]
rs56876287	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6576712	0.81[ASN][1000 genomes]
rs6658034	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6658974	0.96[ASN][1000 genomes]
rs6660306	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6662644	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6662683	0.96[ASN][1000 genomes]
rs6666052	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6666572	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6668752	0.96[ASN][1000 genomes]
rs6669593	0.81[ASN][1000 genomes]
rs6684882	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6688208	0.81[ASN][1000 genomes]
rs6701280	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72948416	0.84[ASN][1000 genomes]
rs7524576	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539413	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541850	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541909	0.96[ASN][1000 genomes]
rs7547208	0.96[ASN][1000 genomes]
rs7551329	0.88[ASN][1000 genomes]
rs7555773	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555821	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr1:84968800-84973200	Active TSS	Right Ventricle	heart
2	chr1:84969000-84973000	Active TSS	Left Ventricle	heart
3	chr1:84969200-84973200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:84969400-84973200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:84969800-84973000	Active TSS	Muscle Satellite Cultured Cells	--
6	chr1:84969800-84973000	Active TSS	Aorta	Aorta
7	chr1:84969800-84973000	Active TSS	HSMM	muscle
8	chr1:84970000-84972800	Active TSS	Ovary	ovary
9	chr1:84970000-84973000	Active TSS	Stomach Smooth Muscle	stomach
10	chr1:84970000-84973200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:84970000-84973200	Active TSS	Fetal Intestine Large	intestine
12	chr1:84970000-84973600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:84970000-84973600	Active TSS	GM12878-XiMat	blood
14	chr1:84970000-84973600	Active TSS	NHLF	lung
15	chr1:84970200-84972800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:84970200-84972800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:84970200-84973000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:84970200-84973000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:84970200-84973000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:84970200-84973000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:84970200-84973000	Active TSS	Fetal Muscle Trunk	muscle
22	chr1:84970200-84973000	Active TSS	HSMMtube	muscle
23	chr1:84970200-84973000	Active TSS	NH-A	brain
24	chr1:84970200-84973200	Active TSS	Psoas Muscle	Psoas
25	chr1:84970200-84973200	Active TSS	NHDF-Ad	bronchial
26	chr1:84970200-84973400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:84970200-84973400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:84970400-84972600	Active TSS	Small Intestine	intestine
29	chr1:84970400-84972800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:84970400-84972800	Active TSS	Osteobl	bone
31	chr1:84970400-84973000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:84970400-84973000	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:84970400-84973000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:84970400-84973000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:84970400-84973000	Active TSS	Fetal Intestine Small	intestine
36	chr1:84970400-84973000	Active TSS	Rectal Smooth Muscle	rectum
37	chr1:84970400-84973000	Active TSS	NHEK	skin
38	chr1:84970400-84973200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr1:84970400-84973200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:84970400-84973200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:84970400-84973400	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr1:84970400-84973600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:84970400-84973600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:84970400-84973600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:84970400-84973600	Active TSS	A549	lung
46	chr1:84970600-84972600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:84970600-84972600	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr1:84970600-84972600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:84970600-84972600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:84970600-84972600	Active TSS	Esophagus	oesophagus

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