Variant report

Variant	rs55815116
Chromosome Location	chr3:160022128-160022129
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	chr3:159994789..159997684-chr3:160020627..160023451,2	MCF-7	breast:
2	chr3:160021318..160023692-chr3:160042324..160044773,2	K562	blood:

Variant related genes	Relation type
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10513550	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920289	0.95[EUR][1000 genomes]
rs12233589	0.95[EUR][1000 genomes]
rs2275153	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305401	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305406	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33999879	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736627	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773371	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272959	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532176	0.81[ASN][1000 genomes]
rs56119270	0.95[EUR][1000 genomes]
rs56124988	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56150006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56401539	0.87[EUR][1000 genomes]
rs57030267	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57050097	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57277659	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57285344	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57555307	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58627305	0.95[EUR][1000 genomes]
rs58654032	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58776572	0.87[EUR][1000 genomes]
rs58915028	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59799252	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60066272	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60153357	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60222090	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60304551	0.83[AFR][1000 genomes]
rs60607858	0.87[EUR][1000 genomes]
rs60703878	0.83[AFR][1000 genomes]
rs60914777	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61066536	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272169	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272176	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272179	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272180	0.95[EUR][1000 genomes]
rs62272181	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272185	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272187	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272188	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272190	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272191	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272193	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272196	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272197	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272198	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272205	0.81[EUR][1000 genomes]
rs62272207	0.95[EUR][1000 genomes]
rs62272231	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272236	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272237	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272245	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272247	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272249	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272251	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272254	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272255	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272256	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272257	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272258	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272259	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272780	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272781	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272783	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272785	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272787	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272788	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272790	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272793	0.80[EUR][1000 genomes]
rs6441307	0.86[AFR][1000 genomes]
rs66769612	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66850724	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764107	0.83[AFR][1000 genomes]
rs6772987	0.83[AFR][1000 genomes]
rs68069205	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154582	0.83[ASN][1000 genomes]
rs73154583	0.83[ASN][1000 genomes]
rs73154587	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155914	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614701	0.95[EUR][1000 genomes]
rs7618017	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645798	0.87[EUR][1000 genomes]
rs7648832	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637414	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
3	chr3:159975000-160025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:159975000-160028000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
11	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:159986400-160024800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:159988200-160030200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:159991000-160024800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:159992400-160035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:159992600-160022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:159992800-160026400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:159992800-160033400	Weak transcription	Fetal Kidney	kidney
19	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:159994600-160025000	Weak transcription	Dnd41	blood
22	chr3:159995000-160024400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:159995400-160034200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:159996400-160037000	Weak transcription	Primary B cells from cord blood	blood
25	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:159996800-160033600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:159997000-160033800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:159997200-160037200	Weak transcription	Brain Angular Gyrus	brain
29	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
30	chr3:159997600-160035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:159999200-160024800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:159999600-160027000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:159999800-160033800	Weak transcription	Aorta	Aorta
34	chr3:159999800-160034000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:159999800-160035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:159999800-160047800	Weak transcription	Lung	lung
37	chr3:160000000-160024800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:160000000-160024800	Weak transcription	Ovary	ovary
39	chr3:160010000-160024800	Weak transcription	Liver	Liver
40	chr3:160010000-160025000	Weak transcription	Left Ventricle	heart
41	chr3:160010000-160033000	Weak transcription	Fetal Intestine Small	intestine
42	chr3:160010000-160034000	Weak transcription	Pancreas	Pancrea
43	chr3:160010000-160047800	Weak transcription	HepG2	liver
44	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:160010200-160024800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:160010200-160034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:160010800-160032000	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:160011800-160023600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:160012200-160033000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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