Variant report

Variant	rs62401766
Chromosome Location	chr6:44101375-44101376
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	GTF2F1	chr6:44101289-44101475	K562	blood:	n/a	n/a
2	TFAP2C	chr6:44101074-44101752	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:44101240-44101390	HCPEpiC	choroid plexus:	n/a	n/a
4	POLR2A	chr6:44100967-44101480	K562	blood:	n/a	n/a
5	FOXA2	chr6:44101069-44102014	HepG2	liver:	n/a	n/a
6	NR2F2	chr6:44100805-44102600	K562	blood:	n/a	n/a
7	POLR2A	chr6:44100927-44101880	SK-N-MC	brain:	n/a	n/a
8	ZNF143	chr6:44100842-44102538	K562	blood:	n/a	chr6:44101529-44101548 chr6:44101576-44101585 chr6:44101563-44101578 chr6:44101574-44101583 chr6:44101567-44101585 chr6:44101562-44101581
9	ZNF143	chr6:44100971-44102000	H1-hESC	embryonic stem cell:	n/a	chr6:44101529-44101548 chr6:44101576-44101585 chr6:44101563-44101578 chr6:44101574-44101583 chr6:44101567-44101585 chr6:44101562-44101581
10	FOXA2	chr6:44101304-44101763	A549	lung:	n/a	n/a
11	ZNF143	chr6:44101349-44101787	Hela-S3	cervix:	n/a	chr6:44101529-44101548 chr6:44101576-44101585 chr6:44101563-44101578 chr6:44101574-44101583 chr6:44101567-44101585 chr6:44101562-44101581
12	POLR2A	chr6:44101371-44101554	HUVEC	blood vessel:	n/a	n/a
13	TEAD4	chr6:44101349-44102441	K562	blood:	n/a	n/a
14	HMGN3	chr6:44101092-44101596	K562	blood:	n/a	n/a
15	SIX5	chr6:44101318-44101768	K562	blood:	n/a	chr6:44101574-44101583 chr6:44101576-44101585
16	HCFC1	chr6:44101181-44102339	K562	blood:	n/a	n/a
17	STAT3	chr6:44101336-44101536	MCF10A-Er-Src	breast:	n/a	chr6:44101478-44101490
18	YY1	chr6:44101211-44101603	HepG2	liver:	n/a	chr6:44101453-44101467
19	POLR2A	chr6:44101132-44101713	GM12892	blood:	n/a	n/a
20	POLR2A	chr6:44101333-44102577	K562	blood:	n/a	n/a
21	FOXA1	chr6:44101343-44101845	HepG2	liver:	n/a	n/a
22	TFAP2A	chr6:44101295-44101765	Hela-S3	cervix:	n/a	chr6:44101515-44101526 chr6:44101515-44101526 chr6:44101511-44101526 chr6:44101515-44101526 chr6:44101515-44101526
23	HCFC1	chr6:44101025-44101953	Hela-S3	cervix:	n/a	n/a
24	SIX5	chr6:44101369-44101649	K562	blood:	n/a	chr6:44101574-44101583 chr6:44101576-44101585
25	ELF1	chr6:44101328-44101738	HepG2	liver:	n/a	n/a
26	FOXA1	chr6:44101343-44101740	HepG2	liver:	n/a	n/a
27	MAX	chr6:44101195-44101722	K562	blood:	n/a	n/a
28	JUND	chr6:44101294-44102423	K562	blood:	n/a	chr6:44102133-44102141
29	MAZ	chr6:44101310-44101622	GM12878	blood:	n/a	n/a
30	SIX5	chr6:44101356-44101749	GM12878	blood:	n/a	chr6:44101574-44101583 chr6:44101576-44101585
31	YY1	chr6:44101370-44101673	SK-N-SH_RA	brain:	n/a	chr6:44101453-44101467
32	SIX5	chr6:44101372-44101727	K562	blood:	n/a	chr6:44101574-44101583 chr6:44101576-44101585
33	ETS1	chr6:44101300-44101677	A549	lung:	n/a	chr6:44101574-44101587 chr6:44101575-44101582 chr6:44101573-44101586
34	JUN	chr6:44099548-44103069	K562	blood:	n/a	chr6:44102133-44102141 chr6:44100938-44100952
35	TBP	chr6:44101375-44101679	K562	blood:	n/a	n/a
36	EP300	chr6:44101342-44101604	SK-N-SH_RA	brain:	n/a	chr6:44101480-44101493
37	EP300	chr6:44101314-44101611	SK-N-SH_RA	brain:	n/a	chr6:44101480-44101493
38	MAX	chr6:44101338-44101728	K562	blood:	n/a	n/a
39	POLR2A	chr6:44099449-44101712	GM12878	blood:	n/a	n/a
40	FOXP2	chr6:44100939-44101681	SK-N-MC	brain:	n/a	n/a
41	FOXA1	chr6:44101362-44101755	HepG2	liver:	n/a	n/a
42	YY1	chr6:44101341-44101718	SK-N-SH_RA	brain:	n/a	chr6:44101453-44101467
43	POLR2A	chr6:44101343-44101445	Hela-S3	cervix:	n/a	n/a
44	MAZ	chr6:44101371-44101664	HepG2	liver:	n/a	n/a
45	BHLHE40	chr6:44100975-44101719	K562	blood:	n/a	n/a
46	ZBTB7A	chr6:44100957-44101597	K562	blood:	n/a	n/a
47	MAZ	chr6:44101333-44101619	Hela-S3	cervix:	n/a	n/a
48	MAZ	chr6:44100915-44102465	K562	blood:	n/a	chr6:44101982-44101992
49	ZNF143	chr6:44101276-44101875	GM12878	blood:	n/a	chr6:44101529-44101548 chr6:44101576-44101585 chr6:44101563-44101578 chr6:44101574-44101583 chr6:44101567-44101585 chr6:44101562-44101581
50	MAZ	chr6:44100375-44101844	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:44099546..44105774-chr6:44219938..44225862,7	K562	blood:
2	chr6:44092682..44101478-chr6:44189085..44198306,11	K562	blood:
3	chr6:44100637..44102842-chr6:44230503..44233422,2	MCF-7	breast:
4	chr6:44063954..44064686-chr6:44101030..44101704,2	MCF-7	breast:
5	chr6:44100712..44103659-chr6:44213625..44216259,3	K562	blood:
6	chr6:44099724..44102557-chr6:44186726..44188523,2	K562	blood:
7	chr6:44098943..44101929-chr6:44117025..44119826,2	MCF-7	breast:

Variant related genes	Relation type
TMEM63B	TF binding region
ENSG00000265700	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000112759	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000146232	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10948121	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12191873	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12199128	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12202501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12206251	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206795	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2064639	1.00[AFR][1000 genomes]
rs2064640	1.00[AFR][1000 genomes]
rs2092870	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236061	1.00[AFR][1000 genomes]
rs3734696	0.97[EUR][1000 genomes]
rs3734697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4628095	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711764	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711766	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714738	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4714750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4714759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714761	0.94[ASN][1000 genomes]
rs4714762	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62403189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349270	1.00[AFR][1000 genomes]
rs9349271	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9357432	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369448	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369449	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369450	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369453	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9369454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369456	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369457	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9369459	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9381287	1.00[AFR][1000 genomes]
rs9381294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394984	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44096400-44106600	Weak transcription	Aorta	Aorta
2	chr6:44096600-44101400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr6:44096600-44101400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr6:44096600-44102400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:44096600-44102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:44096600-44102400	Weak transcription	HSMMtube	muscle
7	chr6:44096600-44103200	Weak transcription	Primary B cells from cord blood	blood
8	chr6:44096600-44107200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:44096600-44107400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:44096600-44119400	Weak transcription	Right Atrium	heart
11	chr6:44096800-44101800	Weak transcription	Fetal Brain Female	brain
12	chr6:44096800-44102000	Weak transcription	Primary T cells from cord blood	blood
13	chr6:44096800-44102200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:44096800-44102400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:44096800-44104800	Weak transcription	HSMM	muscle
16	chr6:44096800-44106800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:44096800-44107400	Weak transcription	GM12878-XiMat	blood
18	chr6:44096800-44119400	Weak transcription	HUVEC	blood vessel
19	chr6:44097000-44102600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:44097400-44102200	Weak transcription	Thymus	Thymus
21	chr6:44097800-44102600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:44098000-44102200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:44098000-44102200	Weak transcription	Spleen	Spleen
24	chr6:44098000-44107200	Weak transcription	Dnd41	blood
25	chr6:44098000-44114800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:44098000-44119400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:44098000-44119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:44098400-44102400	Weak transcription	Left Ventricle	heart
29	chr6:44099000-44101800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:44099000-44102200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:44099400-44101600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:44099400-44102000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:44099400-44102200	Enhancers	Colonic Mucosa	Colon
34	chr6:44099400-44102400	Enhancers	Stomach Mucosa	stomach
35	chr6:44099600-44101400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:44099600-44101800	Enhancers	A549	lung
37	chr6:44099600-44102000	Enhancers	Duodenum Mucosa	Duodenum
38	chr6:44099600-44102000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr6:44099600-44102200	Enhancers	Gastric	stomach
40	chr6:44099800-44101600	Enhancers	Esophagus	oesophagus
41	chr6:44099800-44101800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:44099800-44101800	Enhancers	NHDF-Ad	bronchial
43	chr6:44099800-44102200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:44099800-44102200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:44099800-44102600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:44100000-44101400	Weak transcription	Lung	lung
47	chr6:44100000-44101400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr6:44100000-44102000	Enhancers	Small Intestine	intestine
49	chr6:44100000-44102200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:44100000-44102200	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links