Variant report

Variant	rs10492164
Chromosome Location	chr12:9847133-9847134
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	chr12:9846957-9847376	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:9846974-9847397	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:9846794-9849572	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000213443	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10161013	0.86[EUR][1000 genomes]
rs10743828	0.81[EUR][1000 genomes]
rs10772093	1.00[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs10772099	0.83[EUR][1000 genomes]
rs10844656	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11052306	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1108453	1.00[CHD][hapmap]
rs1134543	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835594	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12304982	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs12306074	1.00[ASN][1000 genomes]
rs12820281	0.83[EUR][1000 genomes]
rs12824727	0.85[EUR][1000 genomes]
rs13377908	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13377939	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16914640	0.85[CEU][hapmap];1.00[CHD][hapmap]
rs16923367	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16927874	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17732859	1.00[CHD][hapmap]
rs2080210	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268145	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2401387	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401388	0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34584384	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34633868	0.83[EUR][1000 genomes]
rs35990903	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3922289	0.85[EUR][1000 genomes]
rs4439599	1.00[CHD][hapmap]
rs4611290	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715780	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56980650	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59016059	0.86[EUR][1000 genomes]
rs59210706	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488110	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488120	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488121	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488123	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71447599	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71447600	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7301386	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74062704	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74062708	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74065337	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74065339	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74065340	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962964	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7964917	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7967436	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969022	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7976474	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10492164	POU5F1P3	cis	parietal	SCAN
rs10492164	RP11-75L1.2	cis	Nerve Tibial	GTEx
rs10492164	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10492164	LRP6	cis	parietal	SCAN
rs10492164	LOC283314	cis	cerebellum	SCAN
rs10492164	RP11-75L1.2	cis	Whole Blood	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
4	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
5	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
8	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
11	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:9827200-9847400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:9827200-9847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:9827200-9852400	Weak transcription	Osteobl	bone
17	chr12:9827400-9849000	Weak transcription	A549	lung
18	chr12:9833000-9849000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:9833200-9847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:9835400-9849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:9837000-9847400	Weak transcription	Fetal Brain Female	brain
22	chr12:9837800-9849400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:9838200-9849800	Strong transcription	Fetal Thymus	thymus
24	chr12:9838400-9849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:9838800-9849200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
27	chr12:9839000-9854400	Weak transcription	Lung	lung
28	chr12:9839400-9848800	Weak transcription	Brain Substantia Nigra	brain
29	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
30	chr12:9840000-9849000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:9840200-9848200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:9840400-9847800	Weak transcription	Aorta	Aorta
33	chr12:9840600-9848400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:9840800-9847800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr12:9841000-9849600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:9841200-9847600	Weak transcription	Fetal Intestine Small	intestine
38	chr12:9841200-9847800	Weak transcription	Thymus	Thymus
39	chr12:9841800-9848600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:9841800-9854800	Weak transcription	Right Ventricle	heart
41	chr12:9841800-9863200	Weak transcription	HSMMtube	muscle
42	chr12:9842000-9847400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:9842000-9848200	Strong transcription	Primary B cells from cord blood	blood
44	chr12:9842200-9847200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:9842200-9850800	Weak transcription	Fetal Brain Male	brain
46	chr12:9842600-9848200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr12:9842800-9847200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:9842800-9848400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:9842800-9852200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:9843000-9847600	Strong transcription	GM12878-XiMat	blood

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