Variant report

Variant	rs2107964
Chromosome Location	chr7:2863574-2863575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:2857314..2858833-chr7:2861762..2864042,2	MCF-7	breast:
2	chr7:2848223..2850269-chr7:2862070..2864443,2	MCF-7	breast:
3	chr7:2861025..2862941-chr7:2863044..2865953,2	K562	blood:
4	chr7:2861786..2864969-chr7:2867313..2871458,3	MCF-7	breast:
5	chr7:2861792..2865677-chr7:2882259..2884341,3	K562	blood:
6	chr7:2861472..2864463-chr7:2865444..2867684,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1182155	0.82[CEU][hapmap]
rs1182172	0.90[EUR][1000 genomes]
rs1182174	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1182175	0.89[CHB][hapmap]
rs1182176	0.92[EUR][1000 genomes]
rs1182177	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[EUR][1000 genomes]
rs1182178	0.92[EUR][1000 genomes]
rs1182179	0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes]
rs1182181	0.91[CEU][hapmap];0.89[CHB][hapmap];0.91[EUR][1000 genomes]
rs1182182	0.91[EUR][1000 genomes]
rs1182183	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1182184	0.92[EUR][1000 genomes]
rs1182185	0.90[CEU][hapmap];0.84[CHB][hapmap];0.92[EUR][1000 genomes]
rs1182186	0.93[EUR][1000 genomes]
rs1182187	0.95[EUR][1000 genomes]
rs1182188	0.91[CEU][hapmap];0.89[CHB][hapmap];0.95[EUR][1000 genomes]
rs1182189	0.91[CEU][hapmap];0.84[CHB][hapmap];0.93[EUR][1000 genomes]
rs1182190	0.89[CHB][hapmap]
rs1182191	0.84[CHB][hapmap]
rs1182194	0.84[CHB][hapmap]
rs1182196	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1182198	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1182199	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1182207	0.84[EUR][1000 genomes]
rs1182208	0.89[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1182209	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1183085	0.92[EUR][1000 genomes]
rs11973498	0.86[CEU][hapmap]
rs13243214	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1614791	0.86[CEU][hapmap]
rs1636247	0.88[EUR][1000 genomes]
rs1636249	0.86[CEU][hapmap]
rs1636250	0.86[CEU][hapmap]
rs1636255	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1636264	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1639066	0.82[CEU][hapmap]
rs1713919	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158694	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2248390	0.91[ASN][1000 genomes]
rs2251491	0.91[ASN][1000 genomes]
rs2260230	0.91[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2266922	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2283779	0.89[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2283783	0.91[ASN][1000 genomes]
rs2283784	0.91[ASN][1000 genomes]
rs2527680	0.81[EUR][1000 genomes]
rs2527683	0.84[ASN][1000 genomes]
rs2527684	0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2527687	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2527690	0.95[ASN][1000 genomes]
rs2527692	0.91[ASN][1000 genomes]
rs2527694	0.90[ASN][1000 genomes]
rs2527695	0.90[ASN][1000 genomes]
rs2527696	0.90[ASN][1000 genomes]
rs2533870	0.86[CEU][hapmap]
rs2533878	0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs2533879	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533882	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533884	0.90[EUR][1000 genomes]
rs2644274	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2644275	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2644281	0.86[CEU][hapmap]
rs2644294	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2644295	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2644296	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2644297	0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2644298	0.90[ASN][1000 genomes]
rs2644309	0.85[EUR][1000 genomes]
rs2644312	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35957220	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6970963	0.82[ASN][1000 genomes]
rs6976160	1.00[YRI][hapmap]
rs6978692	0.91[ASN][1000 genomes]
rs757791	0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7777484	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7783400	0.86[CEU][hapmap]
rs7807978	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs798480	0.80[ASN][1000 genomes]
rs798482	0.80[ASN][1000 genomes]
rs798485	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798486	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798487	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs798488	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs798489	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs798490	0.91[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs798491	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs798492	0.86[JPT][hapmap]
rs798493	0.83[EUR][1000 genomes]
rs798494	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs798495	0.83[CEU][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs798497	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs798498	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs798499	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs798500	0.87[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs798502	0.82[CEU][hapmap]
rs798506	0.83[AFR][1000 genomes]
rs798512	0.80[JPT][hapmap]
rs798518	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs798528	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs798548	0.83[CEU][hapmap]
rs798557	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs960273	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][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	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv1019463	chr7:2848448-2881872	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2107964	GNA12	cis	Nerve Tibial	GTEx
rs2107964	GNA12	cis	multi-tissue	Pritchard
rs2107964	LOC392620	cis	multi-tissue	Pritchard
rs2107964	GNA12	cis	Artery Tibial	GTEx
rs2107964	GNA12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2842600-2869400	Weak transcription	Primary T cells from cord blood	blood
2	chr7:2843200-2864400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr7:2843600-2864400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr7:2848600-2864000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:2848800-2874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:2849600-2866000	Enhancers	Placenta	Placenta
7	chr7:2851600-2869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
9	chr7:2854000-2874800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:2855800-2863600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:2857000-2864600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr7:2857000-2865000	Enhancers	Ovary	ovary
13	chr7:2857000-2867000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:2857200-2864200	Enhancers	NHDF-Ad	bronchial
15	chr7:2857200-2865400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:2858000-2864000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:2858200-2863800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr7:2858200-2865600	Enhancers	Right Ventricle	heart
19	chr7:2858200-2868200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:2858400-2864000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr7:2858400-2865600	Enhancers	Left Ventricle	heart
22	chr7:2858600-2863800	Enhancers	HMEC	breast
23	chr7:2858600-2864200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr7:2858600-2864600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr7:2860000-2864800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:2860000-2866000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr7:2860400-2864600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:2860400-2865400	Enhancers	Brain Hippocampus Middle	brain
29	chr7:2860400-2865600	Enhancers	Primary B cells from peripheral blood	blood
30	chr7:2860400-2865600	Enhancers	Spleen	Spleen
31	chr7:2860400-2865600	Enhancers	NHLF	lung
32	chr7:2860600-2863800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:2860600-2865600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:2860600-2865600	Enhancers	Lung	lung
35	chr7:2860800-2863800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:2860800-2863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:2860800-2865400	Enhancers	HSMMtube	muscle
38	chr7:2861000-2867000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr7:2861000-2881800	Weak transcription	Colonic Mucosa	Colon
40	chr7:2861200-2864000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:2861200-2877000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:2861400-2863600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr7:2861400-2863800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:2861400-2863800	Weak transcription	Esophagus	oesophagus
45	chr7:2861400-2863800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:2861400-2863800	Enhancers	NHEK	skin
47	chr7:2861400-2864400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:2861400-2864600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:2861400-2864800	Weak transcription	Fetal Intestine Small	intestine
50	chr7:2861400-2865000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links