Variant report

Variant	rs707829
Chromosome Location	chr6:15329091-15329092
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	EBF1	chr6:15329085-15329678	GM12878	blood:	n/a	chr6:15329482-15329493 chr6:15329481-15329494 chr6:15329483-15329492 chr6:15329483-15329492 chr6:15329257-15329266 chr6:15329255-15329268 chr6:15329256-15329266
2	WRNIP1	chr6:15328994-15329218	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:15328789-15329131	GM12878	blood:	n/a	n/a
4	EBF1	chr6:15329071-15329663	GM12878	blood:	n/a	chr6:15329482-15329493 chr6:15329481-15329494 chr6:15329483-15329492 chr6:15329483-15329492 chr6:15329257-15329266 chr6:15329255-15329268 chr6:15329256-15329266
5	POLR2A	chr6:15327455-15330043	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:15329069-15329091	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:15328901-15329169	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:15328815-15329231	H1-hESC	embryonic stem cell:	n/a	n/a
9	EBF1	chr6:15328910-15329714	GM12878	blood:	n/a	chr6:15329482-15329493 chr6:15329481-15329494 chr6:15329483-15329492 chr6:15329483-15329492 chr6:15329257-15329266 chr6:15329255-15329268 chr6:15329256-15329266

No.	Distal block	Cell Line	Cell type
1	chr6:15320928..15323607-chr6:15325318..15329724,5	K562	blood:
2	chr6:15326922..15329767-chr6:15340745..15343836,3	K562	blood:
3	chr6:15310524..15313443-chr6:15327959..15329867,2	K562	blood:
4	chr6:15314877..15317482-chr6:15328601..15330118,2	K562	blood:

Variant related genes	Relation type
RNU6-645P	TF binding region
ENSG00000201367	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11968075	0.92[AFR][1000 genomes]
rs1474587	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs16876233	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2282816	0.90[JPT][hapmap]
rs2282823	1.00[JPT][hapmap]
rs2299055	1.00[JPT][hapmap]
rs3857641	0.90[YRI][hapmap]
rs3915734	0.81[JPT][hapmap]
rs707828	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];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707831	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]
rs707835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73361576	0.83[AFR][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];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794776	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs794777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794779	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794784	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs794785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.87[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];0.84[AMR][1000 genomes];0.91[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];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs794797	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383048	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[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:123 , 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	chr6:15319400-15335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:15323600-15329600	Weak transcription	Placenta	Placenta
4	chr6:15323800-15330000	Weak transcription	A549	lung
5	chr6:15323800-15337000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:15324000-15330200	Weak transcription	Hela-S3	cervix
7	chr6:15324400-15332400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:15324600-15333000	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:15324800-15333000	Enhancers	Primary B cells from cord blood	blood
10	chr6:15324800-15339800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:15325000-15330400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:15325000-15332600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:15325200-15330000	Enhancers	Fetal Intestine Small	intestine
14	chr6:15325200-15330400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:15325400-15331400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:15325400-15332400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:15325400-15333000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:15325600-15331200	Weak transcription	Liver	Liver
19	chr6:15325600-15331600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:15325600-15332800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:15325800-15330600	Enhancers	Adipose Nuclei	Adipose
22	chr6:15325800-15333000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:15326000-15330200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:15326200-15329600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:15326200-15331800	Enhancers	NHEK	skin
26	chr6:15326400-15329200	Flanking Active TSS	GM12878-XiMat	blood
27	chr6:15326400-15329800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:15326400-15330000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:15326400-15330600	Enhancers	Spleen	Spleen
30	chr6:15326400-15331600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:15326400-15331800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:15326400-15332400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:15326400-15332400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:15326600-15329800	Enhancers	Left Ventricle	heart
35	chr6:15326600-15331600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:15326600-15331600	Enhancers	Ovary	ovary
37	chr6:15326600-15331600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:15326600-15332000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr6:15326600-15332400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:15326600-15333000	Enhancers	Brain Hippocampus Middle	brain
41	chr6:15326800-15329800	Enhancers	Right Atrium	heart
42	chr6:15326800-15329800	Enhancers	Stomach Smooth Muscle	stomach
43	chr6:15326800-15331000	Weak transcription	HepG2	liver
44	chr6:15326800-15331600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr6:15326800-15332200	Enhancers	Brain Cingulate Gyrus	brain
46	chr6:15326800-15333000	Enhancers	Brain Anterior Caudate	brain
47	chr6:15327000-15330200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr6:15327000-15330400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr6:15327000-15331000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:15327200-15329800	Enhancers	Right Ventricle	heart

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