Variant report

Variant	rs2504163
Chromosome Location	chr6:34893398-34893399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34887346..34889807-chr6:34892795..34896039,3	MCF-7	breast:
2	chr6:34891713..34895604-chr6:34895784..34899746,4	K562	blood:
3	chr6:34856254..34858967-chr6:34891774..34893975,2	MCF-7	breast:
4	chr6:34893096..34895778-chr6:34897349..34899496,2	MCF-7	breast:
5	chr6:34893290..34895416-chr6:34950224..34952119,2	K562	blood:
6	chr6:34892877..34895013-chr6:34901039..34903046,2	K562	blood:

Variant related genes	Relation type
ENSG00000064999	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs16894959	0.94[GIH][hapmap]
rs1737726	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997775	1.00[CEU][hapmap];1.00[CHD][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997776	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473614	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504165	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689090	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2820239	1.00[TSI][hapmap]
rs4646925	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs847854	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847855	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847856	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296140	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462016	1.00[CEU][hapmap]
rs9469919	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9469926	1.00[CEU][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34872400-34907200	Weak transcription	Small Intestine	intestine
2	chr6:34874800-34896000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:34877800-34921000	Weak transcription	Pancreas	Pancrea
4	chr6:34878000-34896400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:34879600-34896800	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:34880800-34893400	Weak transcription	Fetal Thymus	thymus
7	chr6:34881000-34898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:34881200-34928200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:34881400-34896600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:34881400-34902800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:34885200-34894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:34885600-34894400	Weak transcription	Placenta	Placenta
13	chr6:34885800-34895400	Weak transcription	Gastric	stomach
14	chr6:34885800-34902200	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:34885800-34902400	Weak transcription	Fetal Stomach	stomach
16	chr6:34886400-34902400	Weak transcription	Aorta	Aorta
17	chr6:34886400-34902600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:34886400-34923400	Weak transcription	Primary T cells from cord blood	blood
19	chr6:34887000-34902800	Weak transcription	Lung	lung
20	chr6:34887400-34895400	Weak transcription	Ovary	ovary
21	chr6:34887400-34902400	Weak transcription	Psoas Muscle	Psoas
22	chr6:34887600-34894000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:34887600-34894000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:34887600-34894400	Weak transcription	NHLF	lung
25	chr6:34887600-34902600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:34887800-34894000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:34887800-34894200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:34887800-34894400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:34887800-34895400	Weak transcription	Right Atrium	heart
30	chr6:34887800-34895800	Weak transcription	Fetal Heart	heart
31	chr6:34887800-34896000	Weak transcription	Spleen	Spleen
32	chr6:34888000-34894400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:34888000-34902200	Weak transcription	Adipose Nuclei	Adipose
34	chr6:34889600-34923400	Weak transcription	Primary B cells from cord blood	blood
35	chr6:34890400-34894000	Weak transcription	Right Ventricle	heart
36	chr6:34890400-34894000	Weak transcription	Osteobl	bone
37	chr6:34890400-34894200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:34890400-34894400	Weak transcription	NHDF-Ad	bronchial
39	chr6:34890600-34893400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:34890800-34894200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:34891000-34894000	Weak transcription	HMEC	breast
42	chr6:34891000-34894000	Weak transcription	NHEK	skin
43	chr6:34891200-34894200	Weak transcription	NH-A	brain
44	chr6:34891200-34894400	Enhancers	Colon Smooth Muscle	Colon
45	chr6:34891400-34896800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:34891600-34893800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr6:34891800-34893400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:34891800-34895600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:34892200-34893600	Enhancers	Brain Substantia Nigra	brain
50	chr6:34892200-34893800	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links