Variant report

Variant	rs10012339
Chromosome Location	chr4:159052850-159052851
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:159050953..159052978-chr4:159078591..159080720,2	MCF-7	breast:
2	chr4:159050564..159053243-chr4:159059556..159061367,2	MCF-7	breast:
3	chr4:159050755..159053105-chr4:159053356..159055470,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10008208	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10018872	1.00[JPT][hapmap]
rs10024133	1.00[JPT][hapmap]
rs10028490	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12648410	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1320370	1.00[JPT][hapmap]
rs1320371	1.00[JPT][hapmap]
rs14202	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879659	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346320	1.00[JPT][hapmap]
rs2346321	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2346381	1.00[JPT][hapmap]
rs2346776	1.00[JPT][hapmap]
rs2346780	1.00[JPT][hapmap]
rs2346781	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346784	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881373	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4234917	0.85[CEU][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]
rs4309890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317248	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345228	0.85[CEU][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]
rs4391084	1.00[JPT][hapmap]
rs4472184	1.00[JPT][hapmap]
rs4501266	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582199	1.00[JPT][hapmap]
rs4627913	1.00[JPT][hapmap]
rs4690893	1.00[JPT][hapmap]
rs4691455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691456	1.00[JPT][hapmap]
rs4691457	1.00[JPT][hapmap]
rs4691458	1.00[JPT][hapmap]
rs4691461	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	0.85[CEU][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]
rs6812635	1.00[JPT][hapmap]
rs6820988	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6821598	1.00[JPT][hapmap]
rs6830702	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6832099	1.00[JPT][hapmap]
rs6833198	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6834164	1.00[JPT][hapmap]
rs6849902	1.00[JPT][hapmap]
rs6852646	1.00[JPT][hapmap]
rs6852878	0.87[AMR][1000 genomes];0.90[ASN][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	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10012339	TMEM144	cis	Esophagus Muscularis	GTEx
rs10012339	RP11-597D13.9	cis	Heart Left Ventricle	GTEx
rs10012339	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs10012339	TMEM144	cis	Nerve Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042600-159053400	Weak transcription	Right Atrium	heart
2	chr4:159042600-159053600	Weak transcription	Brain Anterior Caudate	brain
3	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
4	chr4:159042800-159053400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:159042800-159053800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:159042800-159054800	Weak transcription	Fetal Heart	heart
7	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:159045200-159058600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:159045200-159059400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:159046200-159054200	Strong transcription	HUVEC	blood vessel
13	chr4:159046400-159053400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:159046800-159053200	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
16	chr4:159047200-159058600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:159049200-159070000	Weak transcription	Placenta	Placenta
18	chr4:159049400-159053800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:159051000-159053000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:159051000-159061000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:159051600-159056000	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:159051800-159053600	Enhancers	Rectal Smooth Muscle	rectum
23	chr4:159051800-159070600	Weak transcription	Fetal Intestine Large	intestine
24	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
25	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:159052000-159054600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
28	chr4:159052200-159054000	Enhancers	NHDF-Ad	bronchial
29	chr4:159052200-159054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:159052200-159055200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:159052400-159053800	Enhancers	Small Intestine	intestine
34	chr4:159052400-159060200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:159052600-159053000	Weak transcription	HSMM	muscle
36	chr4:159052600-159053400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:159052600-159053400	Weak transcription	Aorta	Aorta
38	chr4:159052600-159060400	Weak transcription	Ovary	ovary
39	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
40	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
41	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
42	chr4:159052800-159053000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:159052800-159053800	Weak transcription	HepG2	liver
44	chr4:159052800-159060200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links