Variant report

Variant	rs11610197
Chromosome Location	chr12:29512940-29512941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:29512918-29513050	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:29489097..29490633-chr12:29512483..29514735,2	K562	blood:
2	chr12:29301582..29303959-chr12:29510766..29513729,2	K562	blood:
3	chr12:29504698..29507288-chr12:29512167..29514486,2	MCF-7	breast:

Variant related genes	Relation type
ERGIC2	TF binding region
ENSG00000257258	Chromatin interaction
ENSG00000064763	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10492377	0.82[CEU][hapmap]
rs10492383	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608616	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609540	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610910	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11611420	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611687	0.84[EUR][1000 genomes]
rs11612172	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613628	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11614129	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11614901	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11615636	0.84[EUR][1000 genomes]
rs12809493	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810064	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810315	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811201	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12811723	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813731	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813789	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12813996	0.84[EUR][1000 genomes]
rs12814180	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12814930	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815222	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816511	0.83[EUR][1000 genomes]
rs12817163	0.83[EUR][1000 genomes]
rs12817578	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817825	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12817985	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12819896	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821498	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12821559	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821708	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823372	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823422	0.84[EUR][1000 genomes]
rs12823485	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12823903	0.84[EUR][1000 genomes]
rs12824407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829666	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830274	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12830493	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12830678	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830906	0.84[EUR][1000 genomes]
rs12831730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832038	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832263	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1988943	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2350312	0.84[EUR][1000 genomes]
rs2882377	0.84[EUR][1000 genomes]
rs35618989	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636563	0.84[EUR][1000 genomes]
rs36126531	0.90[ASN][1000 genomes]
rs3764952	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4369447	1.00[CEU][hapmap]
rs67280216	0.84[EUR][1000 genomes]
rs7134744	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295387	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314594	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7961336	0.84[EUR][1000 genomes]
rs7964254	0.84[EUR][1000 genomes]
rs7979654	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[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	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
4	esv3362202	chr12:29512585-29514583	Strong transcription Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11610197	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs11610197	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs11610197	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11610197	RP11-996F15.2	cis	Thyroid	GTEx
rs11610197	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs11610197	RP11-996F15.2	cis	lung	GTEx
rs11610197	RP11-996F15.2	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 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	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
11	chr12:29485600-29533400	Weak transcription	Gastric	stomach
12	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
13	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:29488800-29532000	Weak transcription	NHLF	lung
15	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
18	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:29492400-29518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:29492800-29519000	Weak transcription	HepG2	liver
21	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:29494400-29517800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
24	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
25	chr12:29496400-29518000	Weak transcription	Brain Anterior Caudate	brain
26	chr12:29496400-29518000	Weak transcription	Thymus	Thymus
27	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:29496600-29517800	Weak transcription	NH-A	brain
29	chr12:29496800-29519000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
31	chr12:29497600-29518200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:29498000-29515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:29499000-29532400	Weak transcription	Fetal Brain Female	brain
34	chr12:29499200-29518200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:29499200-29526600	Weak transcription	Stomach Mucosa	stomach
36	chr12:29500200-29533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:29500600-29517800	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:29500600-29518000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:29501000-29518000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:29502000-29518000	Weak transcription	A549	lung
41	chr12:29502200-29518200	Weak transcription	Hela-S3	cervix
42	chr12:29502800-29517800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:29503000-29513000	Strong transcription	Primary B cells from cord blood	blood
44	chr12:29503200-29518200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:29503400-29532200	Weak transcription	HSMMtube	muscle
46	chr12:29504200-29523000	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:29504200-29525800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:29505000-29516200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:29505000-29532400	Weak transcription	Brain Angular Gyrus	brain
50	chr12:29505200-29524600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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