Variant report

Variant	rs11188019
Chromosome Location	chr10:96313960-96313961
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96304740..96307263-chr10:96312412..96314149,2	MCF-7	breast:
2	chr10:96305075..96307344-chr10:96312057..96315359,3	K562	blood:

Variant related genes	Relation type
ENSG00000119969	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1010570	0.83[LWK][hapmap]
rs10786168	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10786169	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786170	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10882454	0.82[EUR][1000 genomes]
rs10882460	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs10882463	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10882469	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882470	0.83[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs10882471	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882473	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882474	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10882477	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10882481	0.83[EUR][1000 genomes]
rs10882486	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11187937	0.83[EUR][1000 genomes]
rs11187939	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs11187944	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs11187948	0.93[LWK][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs11187952	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs11187960	0.83[JPT][hapmap]
rs11187972	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11187973	0.84[EUR][1000 genomes]
rs11187980	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11187996	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187998	0.80[JPT][hapmap]
rs11188009	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11188012	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11188015	0.84[EUR][1000 genomes]
rs11188016	0.86[EUR][1000 genomes]
rs11188017	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11188026	0.87[EUR][1000 genomes]
rs11188030	0.87[EUR][1000 genomes]
rs11188038	0.84[EUR][1000 genomes]
rs11188039	0.83[EUR][1000 genomes]
rs11188040	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs11188041	0.83[EUR][1000 genomes]
rs11527881	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11592354	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11638	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12218213	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12218216	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12219906	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12220588	0.87[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs12221475	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs12572040	0.90[EUR][1000 genomes]
rs12573638	0.80[JPT][hapmap]
rs12762574	0.86[EUR][1000 genomes]
rs1326838	0.80[EUR][1000 genomes]
rs1326839	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1334595	0.83[JPT][hapmap]
rs1359262	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1359263	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1409655	0.83[JPT][hapmap]
rs1749352	0.82[EUR][1000 genomes]
rs1749356	0.80[JPT][hapmap]
rs1854035	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1886272	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889485	0.85[EUR][1000 genomes]
rs1889486	0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs1931757	1.00[JPT][hapmap]
rs1969815	0.85[CEU][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1977288	0.83[JPT][hapmap]
rs1977289	0.81[EUR][1000 genomes]
rs1977290	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1977291	1.00[JPT][hapmap]
rs1980741	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998591	0.81[LWK][hapmap]
rs2012670	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2095380	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2148553	0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs2265364	0.84[EUR][1000 genomes]
rs2274096	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2274417	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2281791	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2860821	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2860840	0.83[JPT][hapmap]
rs2901765	0.82[EUR][1000 genomes]
rs34814196	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3740358	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3758522	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3758523	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3781262	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4351744	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4421688	0.87[EUR][1000 genomes]
rs480032	0.83[JPT][hapmap]
rs4918333	0.85[EUR][1000 genomes]
rs4918401	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4918402	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4918403	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4918404	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4918409	0.85[CEU][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4918411	0.84[EUR][1000 genomes]
rs4918412	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4918417	0.80[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs4918418	0.84[EUR][1000 genomes]
rs4918419	0.85[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs517784	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs556055	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs6583942	0.83[JPT][hapmap]
rs6583943	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6583944	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6583945	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6583946	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68046102	0.83[EUR][1000 genomes]
rs692872	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs701885	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7068337	0.85[EUR][1000 genomes]
rs7073639	0.83[EUR][1000 genomes]
rs7078236	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7078478	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7078811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7079934	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7083898	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7086462	0.83[YRI][hapmap]
rs7089094	0.82[EUR][1000 genomes]
rs7092129	0.83[JPT][hapmap]
rs7100415	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7393251	0.81[YRI][hapmap]
rs7898330	0.81[EUR][1000 genomes]
rs7906843	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7906968	0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs7913343	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs7921721	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs912466	0.80[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs9420641	0.82[EUR][1000 genomes]
rs955694	0.80[JPT][hapmap]
rs9633699	0.83[AFR][1000 genomes];0.84[EUR][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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11188019	HELLS	cis	cerebellum	SCAN
rs11188019	FGFBP3	cis	cerebellum	SCAN
rs11188019	KIF11	cis	cerebellum	SCAN
rs11188019	C19orf22	trans	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306200-96318600	Weak transcription	Aorta	Aorta
2	chr10:96306400-96314200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr10:96306400-96314400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:96306400-96321200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:96306400-96325400	Weak transcription	Lung	lung
6	chr10:96306400-96330600	Weak transcription	Placenta	Placenta
7	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
9	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:96306400-96371000	Weak transcription	Ovary	ovary
12	chr10:96306600-96314000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:96306600-96349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:96306600-96353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:96306800-96314200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr10:96306800-96314200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr10:96306800-96314400	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:96306800-96314600	Weak transcription	Thymus	Thymus
20	chr10:96306800-96315800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr10:96306800-96317200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr10:96306800-96317200	Weak transcription	Fetal Intestine Large	intestine
23	chr10:96306800-96318600	Weak transcription	HSMM	muscle
24	chr10:96306800-96323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:96306800-96330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:96306800-96348000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr10:96306800-96348200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:96306800-96348400	Weak transcription	Primary B cells from cord blood	blood
29	chr10:96306800-96349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
32	chr10:96307000-96314400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr10:96307000-96314800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:96307000-96358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:96307000-96375000	Weak transcription	Osteobl	bone
36	chr10:96307200-96314000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr10:96307200-96314800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:96307200-96315000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr10:96307200-96315800	Weak transcription	NH-A	brain
40	chr10:96307200-96318600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr10:96307200-96320000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr10:96307200-96371200	Weak transcription	Fetal Brain Male	brain
43	chr10:96307600-96314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:96307600-96314600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:96307600-96314600	Weak transcription	Fetal Brain Female	brain
46	chr10:96307600-96314800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:96307600-96315600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:96307600-96316600	Weak transcription	Fetal Lung	lung
49	chr10:96307600-96318800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:96307600-96325400	Weak transcription	NHLF	lung

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