Variant report

Variant	rs6830702
Chromosome Location	chr4:159076826-159076827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:159076732..159078631-chr4:159080658..159082639,2	MCF-7	breast:
2	chr4:159075615..159078408-chr4:159081390..159084163,2	MCF-7	breast:
3	chr4:159075926..159078246-chr4:159082036..159083759,2	K562	blood:

Variant related genes	Relation type
ENSG00000164125	Chromatin interaction

Extended variants
information (count: 66 )
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];0.92[ASN][1000 genomes]
rs10012339	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];0.86[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];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12648410	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]
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];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1879659	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346381	1.00[JPT][hapmap]
rs2346776	1.00[JPT][hapmap]
rs2346780	1.00[JPT][hapmap]
rs2346781	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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];0.92[ASN][1000 genomes]
rs2881373	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];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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];0.86[ASN][1000 genomes]
rs4309890	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];0.86[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];0.86[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];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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];0.86[ASN][1000 genomes]
rs6812635	1.00[JPT][hapmap]
rs6820988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6821598	1.00[JPT][hapmap]
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];0.92[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];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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	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
4	nsv967692	chr4:159068843-159076875	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6830702	TMEM144	cis	Artery Aorta	GTEx
rs6830702	TMEM144	cis	Whole Blood	GTEx
rs6830702	FAM198B	cis	Whole Blood	GTEx
rs6830702	FAM198B	cis	parietal	SCAN
rs6830702	RP11-597D13.7	cis	Nerve Tibial	GTEx
rs6830702	TMEM144	cis	Esophagus Muscularis	GTEx
rs6830702	RP11-597D13.9	cis	Heart Left Ventricle	GTEx
rs6830702	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs6830702	TMEM144	cis	Nerve Tibial	GTEx
rs6830702	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
3	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
5	chr4:159059000-159077800	Weak transcription	Aorta	Aorta
6	chr4:159062000-159077600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:159062600-159077800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:159062600-159083600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:159063400-159078800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:159066400-159080400	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:159067400-159077200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:159068400-159078200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:159068600-159080400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:159068600-159080400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:159068600-159082000	Weak transcription	Brain Substantia Nigra	brain
16	chr4:159068800-159079400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:159068800-159081000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:159069400-159077000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:159070600-159079800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:159071400-159080400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:159072000-159080000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:159072000-159083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:159072400-159077200	Weak transcription	Fetal Heart	heart
24	chr4:159073400-159077200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:159073400-159077800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:159073400-159080000	Weak transcription	Fetal Stomach	stomach
27	chr4:159073400-159082600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:159073400-159083000	Weak transcription	Pancreas	Pancrea
29	chr4:159074400-159077000	Strong transcription	Ovary	ovary
30	chr4:159075400-159077000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:159075800-159077000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:159076000-159077000	Strong transcription	Adipose Nuclei	Adipose
33	chr4:159076000-159077000	Strong transcription	HepG2	liver
34	chr4:159076200-159077000	Strong transcription	HSMM	muscle
35	chr4:159076400-159077000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:159076400-159077200	Strong transcription	HUVEC	blood vessel
37	chr4:159076400-159078200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:159076400-159079600	Enhancers	Fetal Intestine Small	intestine
39	chr4:159076600-159077000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:159076600-159077000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr4:159076600-159077000	Genic enhancers	HMEC	breast
42	chr4:159076600-159077000	Genic enhancers	HSMMtube	muscle
43	chr4:159076600-159077200	Enhancers	Small Intestine	intestine
44	chr4:159076600-159078000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:159076600-159078000	Enhancers	NH-A	brain
46	chr4:159076600-159080600	Enhancers	Fetal Intestine Large	intestine
47	chr4:159076600-159085200	Enhancers	Colon Smooth Muscle	Colon
48	chr4:159076800-159077000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:159076800-159077000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr4:159076800-159077000	Enhancers	Osteobl	bone

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