Variant report

Variant	rs10743598
Chromosome Location	chr12:9235217-9235218
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	chr12:9233957-9235298	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9233968-9235335	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9233981-9235442	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10771307	0.93[CHD][hapmap]
rs10771308	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10771309	0.93[CHD][hapmap]
rs10842789	0.86[CHD][hapmap]
rs10842839	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842849	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048789	0.93[CHD][hapmap];0.80[MEX][hapmap]
rs11048839	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs113973	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805651	0.93[CHD][hapmap]
rs1805657	0.82[CHB][hapmap]
rs1805662	0.87[CHD][hapmap]
rs1805663	0.93[CHD][hapmap]
rs1805682	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216143	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226379	0.93[CHD][hapmap]
rs226380	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226381	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226382	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226384	0.87[CHD][hapmap]
rs226386	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226387	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226390	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs226392	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226394	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226400	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226401	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226403	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226415	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759277	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882977	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487584	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487585	0.83[CHB][hapmap]
rs669	0.93[CHD][hapmap]
rs71453666	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295733	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955940	0.93[CHD][hapmap]
rs7964085	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7965790	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976808	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10743598	CLEC1B	cis	parietal	SCAN
rs10743598	CLEC1A	cis	cerebellum	SCAN
rs10743598	ZNF705A	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
2	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
3	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
5	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
9	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
11	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
12	chr12:9219800-9235800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:9225600-9236200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:9230800-9240400	Weak transcription	Placenta	Placenta
15	chr12:9230800-9243600	Weak transcription	Colonic Mucosa	Colon
16	chr12:9232000-9236000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:9232200-9264600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:9232400-9236200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:9232400-9242600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:9232400-9244600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:9232600-9236400	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:9233200-9236400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:9234000-9235400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:9234000-9235400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:9234000-9237400	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:9234400-9236800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:9234400-9237800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:9234600-9239400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr12:9234800-9235400	Genic enhancers	Adipose Nuclei	Adipose
30	chr12:9234800-9236200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:9235000-9242800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:9235000-9253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:9235200-9236200	Strong transcription	Liver	Liver
34	chr12:9235200-9236200	Weak transcription	Fetal Lung	lung
35	chr12:9235200-9236200	Strong transcription	HepG2	liver
36	chr12:9235200-9236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:9235200-9236400	Weak transcription	Right Ventricle	heart
38	chr12:9235200-9236600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:9235200-9241200	Weak transcription	Left Ventricle	heart
40	chr12:9235200-9242400	Weak transcription	Aorta	Aorta
41	chr12:9235200-9242400	Weak transcription	Ovary	ovary
42	chr12:9235200-9242800	Weak transcription	Fetal Stomach	stomach
43	chr12:9235200-9242800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:9235200-9242800	Weak transcription	Spleen	Spleen
45	chr12:9235200-9243000	Weak transcription	Lung	lung
46	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links