Variant report

Variant	rs10008208
Chromosome Location	chr4:159063925-159063926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159042649..159044924-chr4:159061563..159064027,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10012339	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	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648410	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]
rs1320370	1.00[JPT][hapmap]
rs1320371	1.00[JPT][hapmap]
rs14202	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879659	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346320	1.00[JPT][hapmap]
rs2346321	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2346381	1.00[JPT][hapmap]
rs2346776	1.00[JPT][hapmap]
rs2346780	1.00[JPT][hapmap]
rs2346781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346784	0.93[CEU][hapmap];1.00[CHB][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]
rs2881373	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]
rs4234917	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4309890	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4317248	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4345228	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4389619	0.87[CEU][hapmap]
rs4391084	1.00[JPT][hapmap]
rs4472184	1.00[JPT][hapmap]
rs4501266	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812635	1.00[JPT][hapmap]
rs6820988	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6821598	1.00[JPT][hapmap]
rs6830702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6832099	1.00[JPT][hapmap]
rs6833198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834164	1.00[JPT][hapmap]
rs6849902	1.00[JPT][hapmap]
rs6852646	1.00[JPT][hapmap]
rs6852878	0.85[AMR][1000 genomes];0.84[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	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10008208	TMEM144	cis	Esophagus Muscularis	GTEx
rs10008208	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs10008208	TMEM144	cis	Nerve Tibial	GTEx
rs10008208	RP11-597D13.9	cis	Heart Left Ventricle	GTEx
rs10008208	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs10008208	TMEM144	cis	Whole Blood	GTEx
rs10008208	TMEM144	cis	Artery Aorta	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
5	chr4:159049200-159070000	Weak transcription	Placenta	Placenta
6	chr4:159051800-159070600	Weak transcription	Fetal Intestine Large	intestine
7	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
8	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
10	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
13	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
14	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
15	chr4:159055600-159076200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:159058200-159064000	Weak transcription	HSMM	muscle
17	chr4:159059000-159077800	Weak transcription	Aorta	Aorta
18	chr4:159059400-159071800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:159059400-159076600	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:159060400-159066000	Weak transcription	Brain Substantia Nigra	brain
21	chr4:159060600-159070800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:159060600-159071200	Weak transcription	Ovary	ovary
23	chr4:159060600-159071400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:159060600-159076600	Weak transcription	HMEC	breast
25	chr4:159060800-159067600	Weak transcription	Brain Anterior Caudate	brain
26	chr4:159061800-159066600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:159062000-159065800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:159062000-159077600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr4:159062600-159064000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:159062600-159077800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:159062600-159083600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:159063200-159071600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:159063400-159066600	Strong transcription	HUVEC	blood vessel
34	chr4:159063400-159078800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr4:159063600-159064000	Strong transcription	HepG2	liver
36	chr4:159063800-159064000	Enhancers	Fetal Heart	heart

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