Variant report

Variant	rs707828
Chromosome Location	chr6:15327559-15327560
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	BCLAF1	chr6:15327249-15327876	GM12878	blood:	n/a	chr6:15327611-15327618
2	BATF	chr6:15327475-15327805	GM12878	blood:	n/a	n/a
3	MAX	chr6:15327451-15328003	K562	blood:	n/a	n/a
4	SMC3	chr6:15327514-15327888	K562	blood:	n/a	n/a
5	TBL1XR1	chr6:15327320-15327719	K562	blood:	n/a	n/a
6	EP300	chr6:15327532-15327821	K562	blood:	n/a	n/a
7	JUND	chr6:15327500-15327850	K562	blood:	n/a	n/a
8	RAD21	chr6:15327295-15328081	SK-N-SH	brain:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
9	MYC	chr6:15327478-15327913	K562	blood:	n/a	n/a
10	TEAD4	chr6:15327454-15327962	K562	blood:	n/a	n/a
11	CTCF	chr6:15327465-15328045	SK-N-SH	brain:	n/a	chr6:15327667-15327685 chr6:15327826-15327839
12	POLR2A	chr6:15327500-15327989	GM12878	blood:	n/a	n/a
13	RAD21	chr6:15327506-15327849	IMR90	lung:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
14	RAD21	chr6:15327526-15327812	K562	blood:	n/a	chr6:15327668-15327687
15	CTCF	chr6:15327500-15327650	HCT-116	colon:	n/a	n/a
16	RAD21	chr6:15327427-15327970	HCT-116	colon:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
17	CTCF	chr6:15327497-15327872	K562	blood:	n/a	chr6:15327667-15327685 chr6:15327826-15327839
18	POLR2A	chr6:15327455-15330043	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr6:15327515-15327784	A549	lung:	n/a	chr6:15327667-15327685
20	RAD21	chr6:15327471-15327804	GM12878	blood:	n/a	chr6:15327668-15327687
21	RAD21	chr6:15327521-15327847	K562	blood:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
22	BHLHE40	chr6:15327304-15327922	GM12878	blood:	n/a	n/a
23	BCLAF1	chr6:15327415-15327889	GM12878	blood:	n/a	chr6:15327611-15327618
24	CEBPB	chr6:15327551-15327715	K562	blood:	n/a	n/a
25	CTCF	chr6:15327540-15327690	HVMF	connective:	n/a	chr6:15327667-15327685
26	CTCF	chr6:15327517-15327854	IMR90	lung:	n/a	chr6:15327667-15327685 chr6:15327826-15327839
27	TEAD4	chr6:15327352-15327982	K562	blood:	n/a	n/a
28	CTCF	chr6:15327472-15327978	K562	blood:	n/a	chr6:15327667-15327685 chr6:15327826-15327839
29	RAD21	chr6:15327484-15327854	SK-N-SH_RA	brain:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
30	GATA1	chr6:15327006-15328031	PBDE	blood:	n/a	chr6:15327606-15327622 chr6:15327610-15327619
31	RAD21	chr6:15327428-15327924	SK-N-SH_RA	brain:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
32	CTCF	chr6:15327555-15327737	SK-N-SH_RA	brain:	n/a	chr6:15327667-15327685
33	WRNIP1	chr6:15326524-15328615	GM12878	blood:	n/a	n/a
34	CHD2	chr6:15327500-15327838	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:15327529-15328174	H1-hESC	embryonic stem cell:	n/a	n/a
36	SMC3	chr6:15327470-15328019	GM12878	blood:	n/a	n/a
37	CTCF	chr6:15327480-15327630	HMEC	breast:	n/a	n/a
38	TAL1	chr6:15327510-15327750	K562	blood:	n/a	n/a
39	CTCF	chr6:15327459-15327838	MCF-7	breast:	n/a	chr6:15327667-15327685
40	CTCF	chr6:15327458-15327922	GM12878	blood:	n/a	chr6:15327667-15327685 chr6:15327826-15327839
41	RAD21	chr6:15327459-15327894	MCF-7	breast:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
42	RAD21	chr6:15327503-15327852	A549	lung:	n/a	chr6:15327668-15327687 chr6:15327825-15327839
43	CTCF	chr6:15327460-15327610	NHEK	skin:	n/a	n/a
44	ZNF384	chr6:15327497-15327718	K562	blood:	n/a	n/a
45	RUNX3	chr6:15327011-15327868	GM12878	blood:	n/a	n/a
46	KAP1	chr6:15327518-15327903	HEK293	kidney:	n/a	n/a
47	MAX	chr6:15327480-15327929	K562	blood:	n/a	n/a
48	POU2F2	chr6:15327403-15327964	GM12878	blood:	n/a	chr6:15327590-15327603 chr6:15327590-15327602
49	CBX3	chr6:15327417-15327944	K562	blood:	n/a	n/a
50	ZC3H11A	chr6:15327486-15327663	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:15320928..15323607-chr6:15325318..15329724,5	K562	blood:
2	chr6:15248004..15250330-chr6:15324617..15327935,3	K562	blood:
3	chr6:15324352..15327227-chr6:15327353..15329031,3	K562	blood:
4	chr6:15327193..15327878-chr6:15390015..15390591,2	K562	blood:
5	chr6:15245706..15248419-chr6:15325592..15327879,2	MCF-7	breast:
6	chr6:15326922..15329767-chr6:15340745..15343836,3	K562	blood:
7	chr6:15325527..15327943-chr6:15329707..15332701,2	K562	blood:

Variant related genes	Relation type
RNU6-645P	TF binding region
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction
ENSG00000201519	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1474587	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2282816	0.90[JPT][hapmap]
rs2282823	1.00[JPT][hapmap]
rs2299055	1.00[JPT][hapmap]
rs3915734	0.81[JPT][hapmap]
rs707829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707838	0.81[CHB][hapmap]
rs707839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs760658	0.90[JPT][hapmap]
rs760659	0.91[JPT][hapmap]
rs794775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794776	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs794777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794779	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794784	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794786	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs794788	0.81[CHB][hapmap]
rs794789	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs794792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794793	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs794795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383048	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15311200-15330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:15314400-15327600	Weak transcription	Aorta	Aorta
3	chr6:15319000-15327600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:15319000-15328600	Weak transcription	HSMM	muscle
5	chr6:15319200-15328000	Weak transcription	Fetal Stomach	stomach
6	chr6:15319200-15329000	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:15319400-15335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:15320200-15327600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:15320400-15328600	Weak transcription	Brain Germinal Matrix	brain
10	chr6:15323200-15328800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:15323600-15327600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:15323600-15327600	Weak transcription	Lung	lung
13	chr6:15323600-15329000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:15323600-15329600	Weak transcription	Placenta	Placenta
15	chr6:15323800-15327600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:15323800-15327600	Weak transcription	Brain Angular Gyrus	brain
17	chr6:15323800-15327600	Weak transcription	NHDF-Ad	bronchial
18	chr6:15323800-15328400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:15323800-15328400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:15323800-15328800	Weak transcription	HSMMtube	muscle
21	chr6:15323800-15329000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:15323800-15330000	Weak transcription	A549	lung
23	chr6:15323800-15337000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr6:15324000-15327600	Weak transcription	Esophagus	oesophagus
25	chr6:15324000-15327600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:15324000-15327600	Weak transcription	HMEC	breast
27	chr6:15324000-15328600	Weak transcription	NHLF	lung
28	chr6:15324000-15330200	Weak transcription	Hela-S3	cervix
29	chr6:15324400-15328400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:15324400-15332400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:15324600-15333000	Enhancers	Primary B cells from peripheral blood	blood
32	chr6:15324800-15333000	Enhancers	Primary B cells from cord blood	blood
33	chr6:15324800-15339800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:15325000-15327800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:15325000-15330400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:15325000-15332600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr6:15325200-15327600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:15325200-15327800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:15325200-15328000	Enhancers	Primary T cells from cord blood	blood
40	chr6:15325200-15330000	Enhancers	Fetal Intestine Small	intestine
41	chr6:15325200-15330400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr6:15325400-15328000	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:15325400-15328000	Enhancers	Fetal Intestine Large	intestine
44	chr6:15325400-15328400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:15325400-15331400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr6:15325400-15332400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:15325400-15333000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:15325600-15329000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:15325600-15331200	Weak transcription	Liver	Liver
50	chr6:15325600-15331600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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