Variant report

Variant	rs707987
Chromosome Location	chr6:4059379-4059380
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	POLR2A	chr6:4059306-4059759	SK-N-SH	brain:	n/a	n/a
2	FOSL1	chr6:4059345-4059661	K562	blood:	n/a	n/a
3	MYC	chr6:4059284-4059744	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:4059333-4059785	MCF10A-Er-Src	breast:	n/a	chr6:4059572-4059583 chr6:4059690-4059699
5	JUND	chr6:4059219-4059941	SK-N-SH	brain:	n/a	chr6:4059690-4059699
6	FOSL2	chr6:4059246-4059833	A549	lung:	n/a	chr6:4059690-4059699
7	EP300	chr6:4059273-4059939	SK-N-SH	brain:	n/a	chr6:4059816-4059826
8	JUN	chr6:4059234-4060480	K562	blood:	n/a	chr6:4059690-4059699
9	RXRA	chr6:4059270-4059896	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr6:4059349-4059695	SK-N-SH_RA	brain:	n/a	n/a
11	HDAC2	chr6:4059307-4059664	HepG2	liver:	n/a	n/a
12	FOSL2	chr6:4059376-4059686	A549	lung:	n/a	n/a
13	FOSL2	chr6:4059315-4059739	HepG2	liver:	n/a	chr6:4059690-4059699
14	FOSL2	chr6:4059260-4059842	HepG2	liver:	n/a	chr6:4059690-4059699
15	POLR2A	chr6:4059373-4059721	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr6:4059361-4059708	MCF10A-Er-Src	breast:	n/a	n/a
17	MYBL2	chr6:4059284-4059849	HepG2	liver:	n/a	n/a
18	CTCF	chr6:4059320-4059470	Caco-2	colon:	n/a	n/a
19	IRF1	chr6:4059124-4059449	K562	blood:	n/a	n/a
20	TCF12	chr6:4059180-4059949	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr6:4059319-4059950	K562	blood:	n/a	n/a
22	EP300	chr6:4059346-4059772	HepG2	liver:	n/a	n/a
23	SP1	chr6:4059309-4059761	A549	lung:	n/a	n/a
24	NFIC	chr6:4059166-4059867	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr6:4059226-4059950	SK-N-SH	brain:	n/a	chr6:4059579-4059589
26	EP300	chr6:4059360-4059773	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr6:4059332-4059700	IMR90	lung:	n/a	n/a
28	CTCF	chr6:4059340-4059490	WI-38	lung:	n/a	n/a
29	MYC	chr6:4059370-4059745	MCF10A-Er-Src	breast:	n/a	n/a
30	TCF12	chr6:4059280-4059728	A549	lung:	n/a	n/a
31	TCF12	chr6:4059160-4059959	SK-N-SH	brain:	n/a	n/a
32	ETS1	chr6:4059325-4059682	A549	lung:	n/a	chr6:4059577-4059588 chr6:4059575-4059589
33	FOS	chr6:4059239-4059790	HUVEC	blood vessel:	n/a	chr6:4059572-4059583 chr6:4059690-4059699
34	CTCF	chr6:4059240-4059390	WI-38	lung:	n/a	n/a
35	JUND	chr6:4059222-4059922	SK-N-SH	brain:	n/a	chr6:4059690-4059699
36	MAX	chr6:4059365-4059694	NB4	blood:	n/a	n/a
37	SP1	chr6:4059271-4059917	A549	lung:	n/a	n/a
38	FOS	chr6:4059339-4059835	MCF10A-Er-Src	breast:	n/a	chr6:4059572-4059583 chr6:4059690-4059699
39	ARID3A	chr6:4059355-4059765	K562	blood:	n/a	n/a
40	MAX	chr6:4059341-4059708	K562	blood:	n/a	n/a
41	POLR2A	chr6:4059239-4059925	HepG2	liver:	n/a	n/a
42	CTCF	chr6:4059360-4059510	AG04450	lung:	n/a	n/a
43	CTCF	chr6:4059340-4059490	HFF-Myc	foreskin:	n/a	n/a
44	CTCF	chr6:4059360-4059510	GM12875	blood:	n/a	n/a
45	FOS	chr6:4059357-4059766	MCF10A-Er-Src	breast:	n/a	chr6:4059572-4059583 chr6:4059690-4059699
46	JUND	chr6:4059243-4059916	SK-N-SH	brain:	n/a	chr6:4059690-4059699
47	PBX3	chr6:4059258-4059920	SK-N-SH	brain:	n/a	n/a
48	STAT3	chr6:4059343-4059735	MCF10A-Er-Src	breast:	n/a	n/a
49	CTCF	chr6:4059340-4059490	HEEpiC	esophagus:	n/a	n/a
50	FOSL2	chr6:4059268-4059942	SK-N-SH	brain:	n/a	chr6:4059690-4059699

No.	Distal block	Cell Line	Cell type
1	chr6:4040955..4045707-chr6:4056854..4061183,4	K562	blood:
2	chr6:4054760..4058464-chr6:4059155..4063115,3	K562	blood:
3	chr6:4020118..4022120-chr6:4056131..4059470,3	K562	blood:

Variant related genes	Relation type
PRPF4B	TF binding region
ENSG00000112739	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12174184	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408457	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543355	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181894	0.88[ASN][1000 genomes]
rs2745451	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2745452	0.89[EUR][1000 genomes]
rs3747761	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747762	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747763	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3761787	0.95[ASN][1000 genomes]
rs4466281	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4959916	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4959918	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4959919	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6900476	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905475	0.89[ASN][1000 genomes]
rs6906467	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6910519	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914180	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6916982	0.88[ASN][1000 genomes]
rs6921738	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6930892	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6933593	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6941706	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs697745	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707980	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707981	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707982	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707983	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707984	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707985	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707988	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73349780	0.89[ASN][1000 genomes]
rs7744603	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7763233	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853396	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853397	0.90[ASN][1000 genomes]
rs853398	0.99[ASN][1000 genomes]
rs853399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853400	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853402	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853403	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853404	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853409	0.87[ASN][1000 genomes]
rs853410	0.90[ASN][1000 genomes]
rs853411	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328215	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9328216	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9392547	0.82[EUR][1000 genomes]
rs9392548	0.82[EUR][1000 genomes]
rs9405693	0.82[EUR][1000 genomes]
rs9405694	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs941443	0.88[ASN][1000 genomes]
rs942474	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9503893	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1034223	chr6:4030708-4060347	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
4	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:4035600-4063600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:4035600-4064200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr6:4035800-4064600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr6:4035800-4065000	Strong transcription	Dnd41	blood
14	chr6:4035800-4066000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:4035800-4066000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr6:4035800-4066200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:4036000-4066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:4036000-4066600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:4037200-4059400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr6:4037200-4066200	Strong transcription	Liver	Liver
21	chr6:4037400-4059400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:4037400-4065800	Strong transcription	Placenta	Placenta
23	chr6:4037600-4066200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr6:4037600-4066400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:4037800-4059400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:4038800-4066000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:4040800-4065400	Strong transcription	GM12878-XiMat	blood
28	chr6:4042000-4066400	Strong transcription	Adipose Nuclei	Adipose
29	chr6:4048200-4063600	Strong transcription	Left Ventricle	heart
30	chr6:4048200-4063600	Strong transcription	Thymus	Thymus
31	chr6:4048200-4064000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:4048200-4064600	Strong transcription	Fetal Intestine Large	intestine
33	chr6:4048200-4065800	Strong transcription	Fetal Muscle Leg	muscle
34	chr6:4048600-4063800	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr6:4049800-4062800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:4050200-4059800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:4050200-4060200	Weak transcription	Spleen	Spleen
38	chr6:4051800-4059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:4052000-4067000	Strong transcription	Primary B cells from cord blood	blood
40	chr6:4052400-4067400	Weak transcription	Psoas Muscle	Psoas
41	chr6:4053600-4062400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:4054200-4059400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:4054400-4059400	Weak transcription	Esophagus	oesophagus
44	chr6:4054400-4059400	Weak transcription	Pancreas	Pancrea
45	chr6:4055400-4059400	Weak transcription	Right Ventricle	heart
46	chr6:4056000-4061200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:4056000-4065600	Strong transcription	Fetal Kidney	kidney
48	chr6:4056200-4059400	Weak transcription	Brain Angular Gyrus	brain
49	chr6:4056200-4066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:4056400-4060000	Weak transcription	Fetal Heart	heart

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