Variant report

Variant	rs7953619
Chromosome Location	chr12:29519164-29519165
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29516247..29519208-chr12:29526814..29530124,4	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006410	1.00[YRI][hapmap]
rs10082956	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10128781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1035606	0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1035607	0.86[EUR][1000 genomes]
rs10743652	0.86[YRI][hapmap]
rs10743656	1.00[YRI][hapmap]
rs10843390	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843391	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843397	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11050168	1.00[YRI][hapmap]
rs11050175	0.83[CEU][hapmap]
rs11050209	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1156242	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831751	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288128	1.00[YRI][hapmap]
rs2288129	1.00[YRI][hapmap]
rs3782505	1.00[YRI][hapmap]
rs3782513	0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3815843	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7297435	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7298031	1.00[YRI][hapmap]
rs7299283	1.00[YRI][hapmap]
rs7308534	0.91[YRI][hapmap]
rs7311742	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7964831	1.00[YRI][hapmap]
rs7980218	0.92[YRI][hapmap]
rs9651802	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966541	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996498	0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1796867	chr12:29501941-29524159	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7953619	RP11-996F15.2	cis	Stomach	GTEx
rs7953619	RP11-996F15.2	cis	Artery Aorta	GTEx
rs7953619	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs7953619	ERGIC2	cis	lymphoblastoid	seeQTL
rs7953619	RP11-996F15.2	cis	Artery Tibial	GTEx
rs7953619	IFLTD1	cis	parietal	SCAN
rs7953619	RP11-996F15.2	cis	Whole Blood	GTEx
rs7953619	MLSTD1	cis	normal skin	skin_eQTL
rs7953619	ERGIC2	cis	cerebellum	SCAN
rs7953619	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs7953619	RP11-996F15.2	cis	Thyroid	GTEx
rs7953619	ERGIC2	cis	Lymphoblastoid	GTEx
rs7953619	RP11-996F15.2	cis	lung	GTEx
rs7953619	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs7953619	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs7953619	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs7953619	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
4	chr12:29473800-29522600	Weak transcription	NHEK	skin
5	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
6	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
9	chr12:29485600-29533400	Weak transcription	Gastric	stomach
10	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
11	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:29488800-29532000	Weak transcription	NHLF	lung
13	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
16	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
19	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
20	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
22	chr12:29499000-29532400	Weak transcription	Fetal Brain Female	brain
23	chr12:29499200-29526600	Weak transcription	Stomach Mucosa	stomach
24	chr12:29500200-29533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:29503400-29532200	Weak transcription	HSMMtube	muscle
26	chr12:29504200-29523000	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:29504200-29525800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:29505000-29532400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:29505200-29524600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:29507600-29532200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:29509400-29521600	Weak transcription	Left Ventricle	heart
32	chr12:29509400-29529800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:29510200-29532600	Weak transcription	Fetal Stomach	stomach
34	chr12:29510400-29533400	Weak transcription	Lung	lung
35	chr12:29510800-29520800	Weak transcription	Brain Germinal Matrix	brain
36	chr12:29511600-29532200	Weak transcription	HMEC	breast
37	chr12:29513000-29525800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:29513600-29525000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:29513800-29524600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:29514600-29524600	Strong transcription	Dnd41	blood
41	chr12:29514800-29519800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:29515400-29523000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:29515400-29524600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:29515400-29524600	Strong transcription	Primary B cells from cord blood	blood
45	chr12:29515400-29524600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:29515600-29524800	Strong transcription	Placenta	Placenta
47	chr12:29515600-29532200	Weak transcription	Fetal Intestine Small	intestine
48	chr12:29516000-29533200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:29516600-29525200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr12:29516800-29520000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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