Variant report

Variant	rs17138859
Chromosome Location	chr6:4804469-4804470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4774443..4775951-chr6:4803509..4806203,2	MCF-7	breast:
2	chr6:4777710..4780092-chr6:4801744..4804702,2	K562	blood:
3	chr6:4645018..4646864-chr6:4803237..4804893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11967994	1.00[CHB][hapmap]
rs11968021	1.00[CHB][hapmap]
rs1265332	0.91[CHB][hapmap]
rs1265333	0.91[CHB][hapmap]
rs1265335	1.00[CHB][hapmap]
rs13199417	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs13212871	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1557032	1.00[EUR][1000 genomes]
rs17138856	0.91[CHB][hapmap]
rs17138931	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17138959	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs17138966	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs184588	1.00[CHB][hapmap]
rs2235429	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2326553	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs233476	1.00[CHB][hapmap]
rs3748078	0.91[CHB][hapmap]
rs4376391	1.00[EUR][1000 genomes]
rs56278978	1.00[EUR][1000 genomes]
rs58368827	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60609172	1.00[EUR][1000 genomes]
rs60949901	1.00[EUR][1000 genomes]
rs61278797	1.00[EUR][1000 genomes]
rs6916304	1.00[EUR][1000 genomes]
rs6916467	1.00[EUR][1000 genomes]
rs6919412	1.00[EUR][1000 genomes]
rs73348319	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73348345	1.00[EUR][1000 genomes]
rs73348361	1.00[EUR][1000 genomes]
rs73362530	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73362564	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364523	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364567	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73364571	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7743735	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768749	1.00[EUR][1000 genomes]
rs811251	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs947151	1.00[EUR][1000 genomes]
rs9502239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9502244	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9502247	1.00[EUR][1000 genomes]
rs9502248	1.00[EUR][1000 genomes]
rs9502249	1.00[EUR][1000 genomes]
rs9502250	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs9502251	0.87[EUR][1000 genomes]
rs9504254	0.91[CHB][hapmap]
rs9504262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9504267	0.88[ASN][1000 genomes]
rs9504269	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9504270	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9504271	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9504275	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9504276	1.00[EUR][1000 genomes]
rs9504281	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9504284	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs9504286	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4787400-4808800	Weak transcription	Aorta	Aorta
2	chr6:4794800-4818800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:4795000-4806200	Weak transcription	Gastric	stomach
4	chr6:4795200-4806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:4800000-4810400	Weak transcription	Fetal Intestine Small	intestine
6	chr6:4801000-4805000	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:4801000-4805600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:4801600-4804800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr6:4801800-4804600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:4801800-4805000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:4801800-4805200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:4801800-4805200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:4801800-4805200	Enhancers	Psoas Muscle	Psoas
14	chr6:4801800-4811600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:4802000-4805000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:4802200-4804800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr6:4802200-4811200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:4802400-4804600	Enhancers	K562	blood
19	chr6:4802400-4805000	Enhancers	Right Atrium	heart
20	chr6:4802400-4805200	Enhancers	Lung	lung
21	chr6:4802400-4806200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:4802400-4807000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:4802400-4807400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:4802400-4810400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:4802400-4812000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:4802400-4818800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:4802600-4805000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:4802600-4805000	Enhancers	Right Ventricle	heart
29	chr6:4802800-4804600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr6:4802800-4805000	Enhancers	Brain Substantia Nigra	brain
31	chr6:4802800-4805800	Weak transcription	Fetal Brain Male	brain
32	chr6:4802800-4806200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:4803000-4804600	Enhancers	Ovary	ovary
34	chr6:4803000-4805000	Enhancers	Left Ventricle	heart
35	chr6:4803000-4805000	Enhancers	HepG2	liver
36	chr6:4803000-4805200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:4803000-4805200	Enhancers	Placenta	Placenta
38	chr6:4803200-4804600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:4803200-4804600	Enhancers	Pancreas	Pancrea
40	chr6:4803200-4804600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:4803200-4804600	Enhancers	HSMM	muscle
42	chr6:4803200-4804800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:4803200-4804800	Enhancers	Spleen	Spleen
44	chr6:4803200-4805000	Enhancers	Brain Anterior Caudate	brain
45	chr6:4803200-4805000	Enhancers	Brain Hippocampus Middle	brain
46	chr6:4803200-4805000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:4803200-4805000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:4803200-4805000	Enhancers	HMEC	breast
49	chr6:4803200-4805000	Enhancers	NHEK	skin
50	chr6:4803200-4805200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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