Variant report

Variant	rs6849902
Chromosome Location	chr4:159089861-159089862
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	chr4:159089683-159089877	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:159089656-159090278	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr4:159089656-159089915	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159071408..159073828-chr4:159088522..159091495,2	MCF-7	breast:

Variant related genes	Relation type
FAM198B	TF binding region
ENSG00000248429	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10005007	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10007737	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008208	1.00[JPT][hapmap]
rs10012339	1.00[JPT][hapmap]
rs10016822	0.96[AMR][1000 genomes]
rs10018872	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10024133	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10026876	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028490	1.00[JPT][hapmap]
rs10517689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100150	0.90[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11100151	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11937022	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938464	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12502811	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12511679	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645131	1.00[JPT][hapmap]
rs12648410	1.00[JPT][hapmap]
rs1320370	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320371	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs14202	1.00[JPT][hapmap]
rs17036927	1.00[CEU][hapmap]
rs2346319	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2346320	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346321	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2346381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346774	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2346776	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346780	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346783	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28499342	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28691778	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28719822	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881373	1.00[JPT][hapmap]
rs2881473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4234917	1.00[JPT][hapmap]
rs4317248	1.00[JPT][hapmap]
rs4324593	0.84[EUR][1000 genomes]
rs4345228	1.00[JPT][hapmap]
rs4391084	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472184	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4501266	1.00[JPT][hapmap]
rs4582199	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4627913	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4690893	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691455	1.00[JPT][hapmap]
rs4691456	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4691457	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4691458	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4691459	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691461	1.00[JPT][hapmap]
rs4691462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691464	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691465	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691467	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6536299	1.00[JPT][hapmap]
rs6812635	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813306	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819576	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820988	1.00[JPT][hapmap]
rs6821598	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6830702	1.00[JPT][hapmap]
rs6832099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833198	1.00[JPT][hapmap]
rs6834164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6855420	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671094	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671501	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671934	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7686997	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180159	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8370	1.00[JPT][hapmap]

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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:159083000-159091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:159083400-159090400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:159084200-159090000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:159084200-159090800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:159085000-159095200	Active TSS	Aorta	Aorta
7	chr4:159085200-159094000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr4:159085400-159090800	Active TSS	Stomach Smooth Muscle	stomach
9	chr4:159085400-159095000	Active TSS	Right Atrium	heart
10	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr4:159086000-159090800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:159086200-159090600	Weak transcription	NH-A	brain
13	chr4:159086200-159091400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:159086400-159090000	Weak transcription	Lung	lung
15	chr4:159086400-159093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:159087400-159091000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:159087600-159090000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:159087600-159090200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:159087600-159091800	Active TSS	Ovary	ovary
20	chr4:159087800-159090000	Weak transcription	Brain Anterior Caudate	brain
21	chr4:159087800-159090600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:159087800-159090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:159088000-159091000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr4:159088400-159091600	Active TSS	Rectal Smooth Muscle	rectum
25	chr4:159088400-159094400	Active TSS	Right Ventricle	heart
26	chr4:159088600-159090600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:159088600-159092000	Active TSS	Brain Hippocampus Middle	brain
28	chr4:159088600-159094400	Active TSS	Fetal Heart	heart
29	chr4:159089000-159090000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:159089000-159090400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:159089000-159090400	Active TSS	Muscle Satellite Cultured Cells	--
32	chr4:159089000-159092000	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr4:159089000-159092600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:159089000-159092600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:159089000-159094600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr4:159089200-159090800	Enhancers	Brain Substantia Nigra	brain
37	chr4:159089200-159091600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr4:159089200-159091600	Active TSS	NHDF-Ad	bronchial
39	chr4:159089200-159094200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr4:159089400-159090800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:159089600-159090000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr4:159089600-159090200	Flanking Active TSS	HMEC	breast
43	chr4:159089600-159090200	Flanking Active TSS	HUVEC	blood vessel
44	chr4:159089600-159090400	Flanking Active TSS	Fetal Stomach	stomach
45	chr4:159089600-159091000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr4:159089600-159092200	Active TSS	Duodenum Mucosa	Duodenum
47	chr4:159089600-159094000	Active TSS	Colon Smooth Muscle	Colon
48	chr4:159089600-159094200	Active TSS	Colonic Mucosa	Colon
49	chr4:159089800-159090000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:159089800-159090000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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