Variant report

Variant	rs6478631
Chromosome Location	chr9:101013842-101013843
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101007016..101010479-chr9:101012839..101014596,3	MCF-7	breast:
2	chr9:100842559..100845315-chr9:101012488..101014157,2	MCF-7	breast:
3	chr19:13263852..13264543-chr9:101013687..101014435,2	Hela-S3	cervix:
4	chr9:100979926..100982589-chr9:101013541..101016209,2	MCF-7	breast:
5	chr9:100965216..100966924-chr9:101011389..101013937,2	K562	blood:
6	chr9:101010268..101015223-chr9:101016008..101021084,8	K562	blood:
7	chr9:100818347..100820083-chr9:101012931..101014892,2	MCF-7	breast:
8	chr9:101011351..101016361-chr9:101016435..101019100,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000267598	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115971	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10123643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10124977	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10760210	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10760216	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10760217	0.97[ASN][1000 genomes]
rs10760218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10818627	0.97[ASN][1000 genomes]
rs10818640	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10818644	0.97[ASN][1000 genomes]
rs10818645	0.97[ASN][1000 genomes]
rs10818646	0.97[ASN][1000 genomes]
rs10818648	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818656	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818658	0.97[ASN][1000 genomes]
rs10818662	0.92[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs10818666	0.97[ASN][1000 genomes]
rs10818667	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10818668	0.90[ASN][1000 genomes]
rs10818672	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10818676	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818677	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818678	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10818689	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10818690	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10818691	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10818692	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10818693	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10818739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10818743	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10985517	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10985580	0.90[ASN][1000 genomes]
rs10985583	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985634	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10985641	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985642	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985653	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985669	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985680	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985689	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985711	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985720	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10985743	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10985745	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10985765	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10985772	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10985808	0.85[CHB][hapmap]
rs10985817	0.85[CHB][hapmap]
rs10985819	0.85[CHB][hapmap]
rs10985825	0.85[CHB][hapmap]
rs10985826	0.85[CHB][hapmap]
rs12237988	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342612	0.87[ASN][1000 genomes]
rs12346750	0.97[ASN][1000 genomes]
rs1435253	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1435257	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1573024	0.97[ASN][1000 genomes]
rs1573025	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766883	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17766913	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935389	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304389	0.85[CHB][hapmap]
rs2304390	0.85[CHB][hapmap]
rs2900380	0.97[ASN][1000 genomes]
rs3780444	0.85[CHB][hapmap]
rs3780445	0.85[CHB][hapmap]
rs4379551	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4742719	0.97[ASN][1000 genomes]
rs4742721	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4742722	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743187	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4743188	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4743192	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743194	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs5010004	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs56262782	0.84[ASN][1000 genomes]
rs62574277	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62574288	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62574300	0.87[ASN][1000 genomes]
rs6478630	0.90[ASN][1000 genomes]
rs67569753	0.90[ASN][1000 genomes]
rs7025781	0.89[ASN][1000 genomes]
rs7032046	0.86[ASN][1000 genomes]
rs7042576	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7045158	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7853442	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7853847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7856392	0.85[CHB][hapmap]
rs7859655	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7867465	0.85[CHB][hapmap]
rs7867834	0.85[CHB][hapmap]
rs7868451	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7869257	0.85[CHB][hapmap]
rs7869364	0.85[CHB][hapmap]
rs7873849	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874856	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs879368	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs879369	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9802466	0.83[AMR][1000 genomes]
rs9802650	0.84[AMR][1000 genomes];0.87[ASN][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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100989600-101016000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:100991400-101015400	Weak transcription	Brain Anterior Caudate	brain
3	chr9:100992200-101016000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:100995000-101016600	Weak transcription	Brain Angular Gyrus	brain
5	chr9:100996000-101016000	Weak transcription	Pancreas	Pancrea
6	chr9:100996200-101017200	Weak transcription	Ovary	ovary
7	chr9:101004200-101015800	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:101004200-101017200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:101005200-101017200	Weak transcription	Brain Germinal Matrix	brain
10	chr9:101006400-101014000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:101006600-101014000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:101006600-101016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:101006800-101016800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:101009000-101017200	Weak transcription	Aorta	Aorta
15	chr9:101009200-101015800	Weak transcription	Stomach Mucosa	stomach
16	chr9:101009200-101016600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:101010200-101014000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:101010200-101014200	Genic enhancers	Osteobl	bone
19	chr9:101010200-101015000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:101010200-101015200	Enhancers	A549	lung
21	chr9:101010200-101015600	Enhancers	NHDF-Ad	bronchial
22	chr9:101010200-101016600	Enhancers	Primary B cells from cord blood	blood
23	chr9:101010400-101014000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:101010400-101014000	Genic enhancers	HSMM	muscle
25	chr9:101010400-101014600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:101010400-101014600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:101010400-101014600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr9:101010400-101014800	Genic enhancers	Lung	lung
29	chr9:101010600-101015400	Genic enhancers	Fetal Intestine Small	intestine
30	chr9:101010600-101017200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr9:101011000-101014400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:101011000-101016600	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:101011600-101014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:101011600-101014000	Genic enhancers	NHEK	skin
35	chr9:101011600-101014800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:101011600-101015200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:101011600-101015200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:101011600-101015400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr9:101011600-101015400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:101011600-101015800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:101011600-101015800	Weak transcription	Fetal Thymus	thymus
42	chr9:101011600-101016600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr9:101011600-101017200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:101011600-101017200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:101011800-101014000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:101011800-101015600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr9:101011800-101016000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:101011800-101016000	Weak transcription	Adipose Nuclei	Adipose
49	chr9:101011800-101016400	Weak transcription	Primary T cells from cord blood	blood
50	chr9:101011800-101016600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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