Variant report

Variant	rs4085876
Chromosome Location	chr6:15429731-15429732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15426395..15428488-chr6:15429543..15431690,2	MCF-7	breast:
2	chr6:15428361..15431112-chr6:15432614..15434598,3	K562	blood:
3	chr6:15421478..15424119-chr6:15428105..15430007,2	MCF-7	breast:
4	chr6:15412621..15415523-chr6:15427766..15430879,3	K562	blood:
5	chr6:15427923..15429748-chr6:15438037..15440441,2	K562	blood:
6	chr6:15424279..15427255-chr6:15429243..15432157,3	K562	blood:
7	chr6:15424906..15426863-chr6:15428621..15431301,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1474588	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2072819	0.80[CEU][hapmap]
rs2072821	0.81[CHB][hapmap]
rs2072822	0.81[CHB][hapmap]
rs2076055	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2237117	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2237118	0.88[EUR][1000 genomes]
rs2237121	0.88[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2237124	0.92[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2237132	0.91[EUR][1000 genomes]
rs2237141	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2237145	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237149	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2237150	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2237153	0.81[CEU][hapmap]
rs2237156	0.84[CEU][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs2237157	0.80[CEU][hapmap]
rs2282821	0.82[CHB][hapmap]
rs2282825	0.91[CHB][hapmap]
rs2282826	0.91[CHB][hapmap]
rs2282827	0.91[CHB][hapmap]
rs2299045	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299048	0.96[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs2299053	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs2299054	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap]
rs3778652	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6459406	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7754701	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7754755	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349979	0.88[EUR][1000 genomes]
rs9358060	0.80[AMR][1000 genomes]
rs9370813	0.84[CEU][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs9370817	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9370819	0.87[EUR][1000 genomes]
rs9383051	0.80[CEU][hapmap]
rs9383054	0.84[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs9383061	0.80[EUR][1000 genomes]
rs9396589	0.81[CHB][hapmap]
rs9464787	0.80[CEU][hapmap]
rs9476820	0.80[CEU][hapmap]
rs9476827	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][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	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
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15417000-15452200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr6:15421400-15432400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:15421600-15430800	Weak transcription	Aorta	Aorta
4	chr6:15422400-15430200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:15422800-15430800	Weak transcription	Gastric	stomach
6	chr6:15422800-15433400	Weak transcription	Colonic Mucosa	Colon
7	chr6:15423600-15432600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:15424200-15430800	Weak transcription	Esophagus	oesophagus
9	chr6:15424600-15442000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:15425000-15430000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr6:15425200-15429800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr6:15425600-15445400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:15425800-15437800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:15426000-15430400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:15426000-15432400	Enhancers	Brain Anterior Caudate	brain
16	chr6:15426000-15434000	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:15426000-15435000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:15426000-15441000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:15426400-15440400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:15426400-15442000	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:15426600-15431600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:15426600-15434400	Enhancers	Fetal Lung	lung
23	chr6:15426800-15433000	Enhancers	Primary B cells from cord blood	blood
24	chr6:15426800-15434800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:15427000-15430000	Enhancers	Fetal Thymus	thymus
26	chr6:15427000-15433000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:15427000-15450800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:15427200-15429800	Enhancers	Left Ventricle	heart
29	chr6:15428000-15429800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr6:15428000-15430600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:15428000-15430800	Weak transcription	Lung	lung
32	chr6:15428000-15430800	Weak transcription	Pancreas	Pancrea
33	chr6:15428000-15431400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:15428000-15431400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:15428000-15431600	Weak transcription	Placenta	Placenta
36	chr6:15428000-15432000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:15428000-15435200	Enhancers	Brain Hippocampus Middle	brain
38	chr6:15428000-15441800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:15428200-15429800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:15428200-15430000	Weak transcription	Liver	Liver
41	chr6:15428200-15430000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:15428200-15430400	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:15428200-15430800	Weak transcription	Small Intestine	intestine
44	chr6:15428200-15431000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:15428200-15431600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:15428200-15431600	Weak transcription	Spleen	Spleen
47	chr6:15428200-15431800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:15428200-15432000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:15428200-15432200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:15428200-15432600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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