Variant report

Variant	rs12648410
Chromosome Location	chr4:159094786-159094787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10008208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10012339	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10018872	1.00[JPT][hapmap]
rs10024133	1.00[JPT][hapmap]
rs10028490	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10517689	1.00[JPT][hapmap]
rs11100151	1.00[JPT][hapmap]
rs11938464	1.00[JPT][hapmap]
rs12502811	1.00[JPT][hapmap]
rs12511679	1.00[JPT][hapmap]
rs12645131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1320370	1.00[JPT][hapmap]
rs1320371	1.00[JPT][hapmap]
rs14202	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879659	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2346320	1.00[JPT][hapmap]
rs2346321	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346381	1.00[JPT][hapmap]
rs2346776	1.00[JPT][hapmap]
rs2346780	1.00[JPT][hapmap]
rs2346781	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2346784	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2881373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234917	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4309890	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4317248	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4345228	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4389619	0.86[CEU][hapmap]
rs4391084	1.00[JPT][hapmap]
rs4472184	1.00[JPT][hapmap]
rs4501266	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4582199	1.00[JPT][hapmap]
rs4627913	1.00[JPT][hapmap]
rs4690893	1.00[JPT][hapmap]
rs4691455	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4691456	1.00[JPT][hapmap]
rs4691457	1.00[JPT][hapmap]
rs4691458	1.00[JPT][hapmap]
rs4691461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4691462	1.00[JPT][hapmap]
rs4691463	1.00[JPT][hapmap]
rs4691464	1.00[JPT][hapmap]
rs4691465	1.00[JPT][hapmap]
rs4691467	1.00[JPT][hapmap]
rs6536299	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6812635	1.00[JPT][hapmap]
rs6820988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6821598	1.00[JPT][hapmap]
rs6830702	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832099	1.00[JPT][hapmap]
rs6833198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6834164	1.00[JPT][hapmap]
rs6844920	0.82[CHB][hapmap]
rs6849902	1.00[JPT][hapmap]
rs6852646	1.00[JPT][hapmap]
rs6852878	0.83[AMR][1000 genomes]
rs6855420	1.00[JPT][hapmap]
rs7671094	1.00[JPT][hapmap]
rs7671501	1.00[JPT][hapmap]
rs7671934	1.00[JPT][hapmap]
rs7695599	1.00[JPT][hapmap]
rs8370	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12648410	TMEM144	cis	Nerve Tibial	GTEx
rs12648410	RP11-597D13.7	cis	Nerve Tibial	GTEx
rs12648410	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs12648410	TMEM144	cis	Artery Aorta	GTEx
rs12648410	FAM198B	cis	parietal	SCAN
rs12648410	RP11-597D13.9	cis	Heart Left Ventricle	GTEx
rs12648410	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs12648410	FAM198B	cis	Whole Blood	GTEx
rs12648410	TMEM144	cis	Esophagus Muscularis	GTEx
rs12648410	TMEM144	cis	Whole Blood	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159085000-159095200	Active TSS	Aorta	Aorta
2	chr4:159085400-159095000	Active TSS	Right Atrium	heart
3	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:159090200-159095000	Active TSS	HSMMtube	muscle
5	chr4:159092600-159095200	Active TSS	Ovary	ovary
6	chr4:159092600-159095200	Weak transcription	Spleen	Spleen
7	chr4:159092600-159096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:159092600-159104000	Weak transcription	Lung	lung
9	chr4:159092800-159097400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:159093400-159095600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:159093800-159095200	Flanking Active TSS	HUVEC	blood vessel
12	chr4:159093800-159095400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr4:159093800-159100000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:159094000-159095000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr4:159094000-159096400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr4:159094000-159097400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:159094000-159097400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:159094000-159097400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:159094200-159094800	Enhancers	Brain Substantia Nigra	brain
20	chr4:159094200-159094800	Enhancers	Stomach Mucosa	stomach
21	chr4:159094200-159094800	Enhancers	Osteobl	bone
22	chr4:159094200-159095000	Enhancers	Brain Angular Gyrus	brain
23	chr4:159094200-159095200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:159094200-159095400	Weak transcription	Left Ventricle	heart
25	chr4:159094200-159095600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:159094200-159097200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:159094200-159097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:159094200-159097200	Weak transcription	Psoas Muscle	Psoas
29	chr4:159094200-159097200	Weak transcription	NH-A	brain
30	chr4:159094200-159097200	Weak transcription	NHEK	skin
31	chr4:159094200-159097400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr4:159094200-159097400	Weak transcription	Pancreas	Pancrea
33	chr4:159094200-159097400	Weak transcription	Small Intestine	intestine
34	chr4:159094200-159099200	Weak transcription	Placenta	Placenta
35	chr4:159094400-159094800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:159094400-159095000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:159094400-159095000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:159094400-159095000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:159094400-159095200	Enhancers	Brain Cingulate Gyrus	brain
40	chr4:159094400-159095200	Flanking Active TSS	Fetal Heart	heart
41	chr4:159094400-159095200	Enhancers	Fetal Stomach	stomach
42	chr4:159094400-159095200	Weak transcription	Right Ventricle	heart
43	chr4:159094400-159095200	Flanking Active TSS	HepG2	liver
44	chr4:159094400-159095400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:159094400-159095400	Enhancers	Rectal Smooth Muscle	rectum
46	chr4:159094400-159096000	Enhancers	Colon Smooth Muscle	Colon
47	chr4:159094400-159096200	Enhancers	Brain Hippocampus Middle	brain
48	chr4:159094400-159096600	Enhancers	Fetal Intestine Small	intestine
49	chr4:159094400-159097200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:159094400-159097200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links