Variant report

Variant	rs16917971
Chromosome Location	chr12:9223242-9223243
allele	A/C
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	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9222798-9223404	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9222191-9223516	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9223053-9223784	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1012588	0.92[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10492114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10492115	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11608867	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11609582	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs11611433	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11613746	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11615091	0.96[ASN][1000 genomes]
rs11615143	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11615434	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11615443	1.00[JPT][hapmap]
rs11834163	0.82[JPT][hapmap]
rs16918162	1.00[JPT][hapmap]
rs1805665	0.85[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805680	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805720	0.85[JPT][hapmap]
rs1863838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs226405	1.00[CHD][hapmap]
rs226406	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226407	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3026229	1.00[CEU][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213832	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3741849	1.00[JPT][hapmap]
rs3741850	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3741852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4882976	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882978	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882979	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882981	0.84[JPT][hapmap]
rs4883213	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56256934	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56345025	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6487609	0.88[ASN][1000 genomes]
rs6487636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6487650	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7302725	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73048097	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73050004	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73050007	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73050013	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73051904	0.88[ASN][1000 genomes]
rs74061406	0.96[ASN][1000 genomes]
rs7955497	0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7965529	0.88[ASN][1000 genomes]
rs7967997	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970135	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9888309	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]

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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16917971	POU5F1P3	cis	cerebellum	SCAN
rs16917971	LAG3	cis	parietal	SCAN
rs16917971	CLECL1	cis	parietal	SCAN
rs16917971	CLEC1B	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9217400-9223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:9217800-9225000	Weak transcription	Small Intestine	intestine
3	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
4	chr12:9218000-9226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:9218200-9224200	Weak transcription	Ovary	ovary
7	chr12:9218200-9232200	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
9	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
10	chr12:9218400-9223800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:9218400-9224200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:9218400-9224200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:9218400-9224600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:9218400-9228600	Weak transcription	Brain Anterior Caudate	brain
15	chr12:9218400-9230800	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:9218400-9231000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:9218400-9234400	Weak transcription	Right Atrium	heart
18	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
20	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:9218600-9225000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:9218600-9229400	Weak transcription	Colonic Mucosa	Colon
23	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
26	chr12:9218800-9225000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:9218800-9230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
30	chr12:9219000-9224000	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:9219000-9233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:9219200-9223600	Weak transcription	Fetal Stomach	stomach
33	chr12:9219200-9224200	Weak transcription	Right Ventricle	heart
34	chr12:9219200-9225000	Weak transcription	Lung	lung
35	chr12:9219200-9226400	Weak transcription	Pancreas	Pancrea
36	chr12:9219200-9229200	Weak transcription	Gastric	stomach
37	chr12:9219200-9234600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
39	chr12:9219400-9233200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:9219600-9224600	Weak transcription	Fetal Intestine Large	intestine
41	chr12:9219800-9225200	Strong transcription	Adipose Nuclei	Adipose
42	chr12:9219800-9233200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:9219800-9235800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:9220000-9224800	Weak transcription	Fetal Intestine Small	intestine
45	chr12:9220200-9225000	Strong transcription	HepG2	liver
46	chr12:9220600-9226200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:9220600-9232600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:9220800-9227000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:9220800-9232400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:9221000-9228600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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