Variant report

Variant	rs3112983
Chromosome Location	chr2:95716644-95716645
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95687101..95691897-chr2:95715547..95720847,7	MCF-7	breast:
2	chr2:95688082..95691737-chr2:95716243..95720139,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172005	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10172167	0.86[CEU][hapmap]
rs17119148	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs1875402	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs2001254	0.83[EUR][1000 genomes]
rs2291991	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2320619	0.94[EUR][1000 genomes]
rs2320620	0.95[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes]
rs2320621	0.83[EUR][1000 genomes]
rs2320624	0.83[EUR][1000 genomes]
rs3105098	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3105099	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3105100	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3105101	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105102	0.81[EUR][1000 genomes]
rs3105104	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3105105	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs3112221	0.84[EUR][1000 genomes]
rs3112222	0.84[EUR][1000 genomes]
rs3112223	0.84[EUR][1000 genomes]
rs3112225	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs3112228	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3112229	0.80[CEU][hapmap]
rs3112230	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs3112231	0.87[EUR][1000 genomes]
rs3112982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3112984	0.94[CEU][hapmap];0.85[CHB][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112985	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112986	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112987	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112990	0.80[ASN][1000 genomes]
rs3112995	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs3112996	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs3112997	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs3113000	0.83[EUR][1000 genomes]
rs3113001	0.83[EUR][1000 genomes]
rs3113002	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4241315	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4555374	0.86[CEU][hapmap]
rs4564804	0.86[CEU][hapmap]
rs4854241	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4854243	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4854244	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4854247	0.81[EUR][1000 genomes]
rs6708474	0.86[CEU][hapmap]
rs6719098	0.81[EUR][1000 genomes]
rs6723333	0.92[EUR][1000 genomes]
rs6725821	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs7560571	0.82[CHB][hapmap]
rs7565772	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs7582368	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[EUR][1000 genomes]
rs7585473	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs872580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9324212	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95705800-95719000	Enhancers	GM12878-XiMat	blood
2	chr2:95705800-95721600	Genic enhancers	Fetal Thymus	thymus
3	chr2:95706200-95723800	Weak transcription	Fetal Kidney	kidney
4	chr2:95706400-95717600	Genic enhancers	Thymus	Thymus
5	chr2:95709400-95720200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:95709600-95724000	Weak transcription	Pancreas	Pancrea
7	chr2:95709800-95718000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:95712600-95720800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:95713600-95719600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:95713600-95719800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:95713800-95719400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:95713800-95719400	Strong transcription	Dnd41	blood
13	chr2:95713800-95719800	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr2:95714400-95717000	Enhancers	Fetal Lung	lung
15	chr2:95714400-95717600	Strong transcription	Primary T cells from cord blood	blood
16	chr2:95714400-95718800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:95714400-95724400	Weak transcription	Gastric	stomach
18	chr2:95715400-95718800	Strong transcription	Brain Substantia Nigra	brain
19	chr2:95715400-95719800	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr2:95715600-95718000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:95715600-95719600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:95715800-95717000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:95716000-95717600	Weak transcription	Esophagus	oesophagus
24	chr2:95716200-95718200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:95716200-95718600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr2:95716200-95723000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr2:95716400-95716800	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:95716400-95716800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:95716400-95716800	Genic enhancers	Brain Hippocampus Middle	brain
30	chr2:95716400-95717200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr2:95716600-95716800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:95716600-95717000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:95716600-95717000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:95716600-95717400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:95716600-95717800	Weak transcription	Placenta	Placenta
36	chr2:95716600-95718400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:95716600-95718800	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links