Variant report

Variant	rs11188040
Chromosome Location	chr10:96355066-96355067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96313161..96315470-chr10:96353062..96355863,2	K562	blood:
2	chr10:96339432..96341136-chr10:96352569..96355112,2	K562	blood:

Variant related genes	Relation type
ENSG00000119969	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1018602	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042192	0.81[LWK][hapmap]
rs1042194	0.81[LWK][hapmap]
rs10786168	0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs10786169	0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs10786170	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10882460	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10882463	0.87[MEX][hapmap]
rs10882470	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10882474	0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs10882477	0.83[EUR][1000 genomes]
rs10882481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187948	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs11187952	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11187972	0.86[CEU][hapmap]
rs11187980	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs11187998	0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap]
rs11188009	0.86[MEX][hapmap];0.81[TSI][hapmap]
rs11188012	0.80[JPT][hapmap]
rs11188015	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11188016	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188017	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188019	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs11188026	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188030	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188038	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11188041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12218213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12218216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12219906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12220588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12221475	0.84[CEU][hapmap]
rs12570013	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573638	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1326838	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1326839	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1359262	0.82[EUR][1000 genomes]
rs1359263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854034	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1854035	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1889486	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1926712	0.84[LWK][hapmap]
rs1931757	0.80[JPT][hapmap]
rs1969815	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1977290	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1977291	0.80[JPT][hapmap]
rs1980741	0.80[JPT][hapmap]
rs2012670	0.85[EUR][1000 genomes]
rs2148553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274096	0.82[EUR][1000 genomes]
rs2274417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281791	0.87[MEX][hapmap]
rs2281890	0.81[LWK][hapmap]
rs2860821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2860838	0.81[LWK][hapmap]
rs34814196	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35390752	0.81[LWK][hapmap]
rs35774063	0.82[EUR][1000 genomes]
rs3740358	0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3758522	0.83[EUR][1000 genomes]
rs3758523	0.84[EUR][1000 genomes]
rs3781262	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4316436	0.82[EUR][1000 genomes]
rs4351744	0.80[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4421688	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4611135	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4918401	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918402	0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4918403	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918404	0.82[EUR][1000 genomes]
rs4918409	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918412	0.83[EUR][1000 genomes]
rs4918417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918418	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493088	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs6583944	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6583945	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6583946	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6583954	0.84[LWK][hapmap]
rs68046102	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692872	0.87[MEX][hapmap]
rs701885	0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7068337	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078478	0.80[JPT][hapmap]
rs7078811	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7079934	0.83[EUR][1000 genomes]
rs7083898	0.80[JPT][hapmap]
rs7086462	0.84[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs7100415	0.81[EUR][1000 genomes]
rs717238	0.84[LWK][hapmap]
rs7393251	0.85[CEU][hapmap]
rs7900135	0.81[LWK][hapmap]
rs7906843	0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7906968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913343	0.83[CEU][hapmap]
rs7921721	0.80[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs912466	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932809	0.84[LWK][hapmap]
rs955694	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv517681	chr10:96343228-96387079	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv975786	chr10:96352319-96359053	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11188040	HELLS	cis	cerebellum	SCAN
rs11188040	KIF11	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
3	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:96306400-96371000	Weak transcription	Ovary	ovary
6	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
9	chr10:96307000-96358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:96307000-96375000	Weak transcription	Osteobl	bone
11	chr10:96307200-96371200	Weak transcription	Fetal Brain Male	brain
12	chr10:96307600-96356000	Weak transcription	NHDF-Ad	bronchial
13	chr10:96307600-96373200	Weak transcription	Brain Germinal Matrix	brain
14	chr10:96307800-96373000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:96308000-96373200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:96309600-96372800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr10:96309600-96377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr10:96312800-96372200	Strong transcription	Dnd41	blood
19	chr10:96314200-96373400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr10:96315000-96369200	Weak transcription	Fetal Kidney	kidney
21	chr10:96316000-96371400	Weak transcription	Fetal Brain Female	brain
22	chr10:96316000-96374000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr10:96316200-96357600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr10:96316200-96373000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:96317000-96372600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:96324000-96356600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:96324000-96376600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:96324200-96365600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr10:96325800-96376000	Weak transcription	NHLF	lung
30	chr10:96331000-96377400	Weak transcription	Placenta	Placenta
31	chr10:96331200-96361800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:96332400-96359200	Weak transcription	Left Ventricle	heart
33	chr10:96335400-96357200	Weak transcription	Small Intestine	intestine
34	chr10:96338800-96372000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:96345400-96360000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:96345400-96360400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:96345400-96371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr10:96345600-96372400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr10:96346200-96355200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr10:96346400-96360000	Strong transcription	Fetal Thymus	thymus
41	chr10:96346600-96360800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:96346600-96372600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr10:96346800-96358800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr10:96346800-96359400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:96347200-96368000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:96347800-96362000	Strong transcription	Hela-S3	cervix
47	chr10:96348000-96355400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr10:96348000-96358200	Strong transcription	HSMM	muscle
49	chr10:96348000-96359200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr10:96348000-96369600	Weak transcription	Fetal Heart	heart

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