Variant report

Variant	rs6507659
Chromosome Location	chr18:43584201-43584202
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	chr18:43578639..43580570-chr18:43582338..43584371,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10468858	0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10468859	0.81[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10468860	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10468978	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10468980	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1048827	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10502871	0.93[CHD][hapmap]
rs12326264	0.86[EUR][1000 genomes]
rs12326492	0.88[EUR][1000 genomes]
rs12604765	0.88[EUR][1000 genomes]
rs12604777	0.88[EUR][1000 genomes]
rs12604854	0.88[EUR][1000 genomes]
rs12604855	0.88[EUR][1000 genomes]
rs12607016	0.88[EUR][1000 genomes]
rs1438388	0.81[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs16978508	0.99[ASN][1000 genomes]
rs16978509	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs16978517	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1837213	0.96[ASN][1000 genomes]
rs2276196	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276197	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276199	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3745001	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3844540	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4081459	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4081460	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4081461	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4121893	0.83[EUR][1000 genomes]
rs4121894	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs486424	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs488431	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4890308	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890309	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890607	0.84[EUR][1000 genomes]
rs4890608	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890609	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890610	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890611	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4890612	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4890613	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4890614	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs495371	0.85[EUR][1000 genomes]
rs497245	0.85[EUR][1000 genomes]
rs55966192	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56663039	0.88[EUR][1000 genomes]
rs567504	0.92[ASN][1000 genomes]
rs568448	0.96[ASN][1000 genomes]
rs57140490	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57141604	0.87[ASN][1000 genomes]
rs57259994	0.88[EUR][1000 genomes]
rs57525917	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57589400	0.88[EUR][1000 genomes]
rs57872016	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58610818	0.88[EUR][1000 genomes]
rs58727515	0.84[EUR][1000 genomes]
rs58786055	0.88[EUR][1000 genomes]
rs58941766	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58976752	0.87[EUR][1000 genomes]
rs591123	0.88[EUR][1000 genomes]
rs59280848	0.86[EUR][1000 genomes]
rs593664	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs594492	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs596415	0.98[ASN][1000 genomes]
rs59766210	0.86[EUR][1000 genomes]
rs60116181	0.88[EUR][1000 genomes]
rs610186	0.91[JPT][hapmap]
rs61066139	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6507653	0.86[EUR][1000 genomes]
rs6507654	0.86[EUR][1000 genomes]
rs6507655	0.86[EUR][1000 genomes]
rs6507656	0.86[EUR][1000 genomes]
rs6507658	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6507661	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs6507662	0.93[CHD][hapmap]
rs654466	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs67746112	0.88[EUR][1000 genomes]
rs687526	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs688547	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7227161	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7229227	0.88[EUR][1000 genomes]
rs7229264	0.88[EUR][1000 genomes]
rs7237564	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7237598	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7237602	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7237813	0.92[ASN][1000 genomes]
rs7240441	0.81[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7240541	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7241551	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7242970	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7243109	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7243407	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7244712	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7244785	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7244810	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72642430	0.88[EUR][1000 genomes]
rs72642431	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72642432	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72642433	0.87[EUR][1000 genomes]
rs72642434	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72642435	0.96[ASN][1000 genomes]
rs73953950	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7408094	0.86[EUR][1000 genomes]
rs8084943	0.88[EUR][1000 genomes]
rs8084952	0.84[EUR][1000 genomes]
rs8097830	0.89[CHD][hapmap]
rs920294	0.88[EUR][1000 genomes]
rs920296	0.88[EUR][1000 genomes]
rs9630785	0.88[EUR][1000 genomes]
rs9675392	0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.96[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	nsv2277	chr18:43543715-43588579	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6507659	HAUS1	cis	parietal	SCAN
rs6507659	PSTPIP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43558800-43608000	Weak transcription	Pancreas	Pancrea
2	chr18:43560400-43597600	Weak transcription	Left Ventricle	heart
3	chr18:43560600-43591600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr18:43562600-43585600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr18:43563400-43592000	Weak transcription	Psoas Muscle	Psoas
6	chr18:43565400-43588800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr18:43565400-43590800	Weak transcription	Colon Smooth Muscle	Colon
8	chr18:43565600-43588800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr18:43567800-43588800	Weak transcription	NHEK	skin
10	chr18:43568600-43596800	Weak transcription	Adipose Nuclei	Adipose
11	chr18:43568800-43588600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr18:43568800-43607800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr18:43569400-43588800	Weak transcription	Fetal Stomach	stomach
14	chr18:43570200-43588800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr18:43571400-43622000	Weak transcription	Gastric	stomach
16	chr18:43574200-43590000	Weak transcription	HMEC	breast
17	chr18:43574200-43592000	Weak transcription	NH-A	brain
18	chr18:43574200-43593200	Weak transcription	NHDF-Ad	bronchial
19	chr18:43574200-43597400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr18:43574200-43608000	Weak transcription	NHLF	lung
21	chr18:43574600-43608000	Weak transcription	Osteobl	bone
22	chr18:43576000-43585800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:43576600-43588800	Weak transcription	Ovary	ovary
24	chr18:43577000-43589600	Weak transcription	Liver	Liver
25	chr18:43578600-43587200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr18:43579000-43587200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr18:43579000-43588600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr18:43579200-43587200	Weak transcription	Spleen	Spleen
29	chr18:43579600-43587400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr18:43579800-43589400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr18:43580000-43592600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:43580600-43587800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:43581400-43590200	Weak transcription	Primary T cells from cord blood	blood
34	chr18:43581400-43590600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr18:43581600-43589400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr18:43582200-43592600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr18:43582400-43588600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr18:43582600-43585400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr18:43583200-43588600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr18:43583200-43589400	Weak transcription	K562	blood
41	chr18:43583200-43590600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr18:43583400-43585200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr18:43583400-43585600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr18:43583400-43587200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:43583400-43587200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr18:43583400-43587400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr18:43583400-43587600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:43583400-43587800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr18:43583400-43587800	Weak transcription	Aorta	Aorta
50	chr18:43583400-43588200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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