Variant report

Variant	rs12219906
Chromosome Location	chr10:96308954-96308955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr10:96308951-96309561	MCF-7	breast:	n/a	n/a
2	POLR2A	chr10:96308879-96309540	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA3	chr10:96308879-96309598	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:96302855..96305210-chr10:96308842..96310359,2	MCF-7	breast:
2	chr10:96304239..96306860-chr10:96307648..96309568,3	K562	blood:
3	chr10:96307893..96310322-chr10:96320531..96323110,2	K562	blood:
4	chr10:96307884..96309770-chr10:96316701..96318335,2	K562	blood:
5	chr10:96304195..96307318-chr10:96307648..96311886,5	K562	blood:
6	chr10:96306294..96309021-chr10:96316197..96318090,2	K562	blood:

No data

Variant related genes	Relation type
HELLS	TF binding region
ENSG00000119969	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1018602	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10786168	0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10786169	0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1079504	0.82[EUR][1000 genomes]
rs10882460	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs10882463	0.87[MEX][hapmap];0.80[TSI][hapmap]
rs10882470	0.84[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs10882473	0.82[EUR][1000 genomes]
rs10882474	0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882477	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882481	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187948	0.84[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs11187952	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs11187958	0.83[EUR][1000 genomes]
rs11187966	0.84[EUR][1000 genomes]
rs11187972	0.86[CEU][hapmap]
rs11187980	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs11187998	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap]
rs11188005	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11188009	0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs11188012	0.80[JPT][hapmap]
rs11188015	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188016	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11188017	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188019	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]
rs11188026	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188030	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188038	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188039	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188040	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]
rs11188041	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs12218213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12218216	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];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12220588	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221475	0.84[CEU][hapmap]
rs12570013	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12573638	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1326838	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1326839	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1359263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1749356	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1854034	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1854035	0.83[EUR][1000 genomes]
rs1889486	0.84[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1926712	0.81[LWK][hapmap]
rs1931757	0.80[JPT][hapmap]
rs1969815	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1977290	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1977291	0.80[JPT][hapmap]
rs1980741	0.80[JPT][hapmap]
rs2012670	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2025445	0.81[LWK][hapmap]
rs2031322	0.81[LWK][hapmap]
rs2148553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265362	0.82[EUR][1000 genomes]
rs2274096	0.85[EUR][1000 genomes]
rs2274417	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];1.00[MKK][hapmap];1.00[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]
rs2281791	0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2296680	0.81[LWK][hapmap]
rs2860760	0.83[EUR][1000 genomes]
rs2860821	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901764	0.82[EUR][1000 genomes]
rs34814196	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774063	0.86[EUR][1000 genomes]
rs3740358	0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs3758522	0.82[EUR][1000 genomes]
rs3758523	0.82[EUR][1000 genomes]
rs3781262	0.84[EUR][1000 genomes]
rs4316436	0.86[EUR][1000 genomes]
rs4351744	0.80[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4421688	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4611135	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4918401	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918402	0.87[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4918403	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918404	0.86[EUR][1000 genomes]
rs4918409	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918411	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918412	0.82[EUR][1000 genomes]
rs4918417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918418	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4918419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs493088	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs522111	0.81[EUR][1000 genomes]
rs542540	0.80[EUR][1000 genomes]
rs56020662	0.84[EUR][1000 genomes]
rs576517	0.81[EUR][1000 genomes]
rs6583944	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583945	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583946	0.84[EUR][1000 genomes]
rs68046102	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs692872	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs701885	0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7068337	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7078478	0.80[JPT][hapmap]
rs7078811	0.80[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7079934	0.87[EUR][1000 genomes]
rs7083898	0.80[JPT][hapmap]
rs7086462	0.84[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs7087472	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs717238	0.81[LWK][hapmap]
rs7393251	0.85[CEU][hapmap]
rs7906843	0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[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];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7913343	0.83[CEU][hapmap]
rs7921721	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs912466	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs932809	0.81[LWK][hapmap]
rs945123	0.80[EUR][1000 genomes]
rs955694	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12219906	KIF11	cis	cerebellum	SCAN
rs12219906	HELLS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96304400-96309000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:96306200-96318600	Weak transcription	Aorta	Aorta
3	chr10:96306400-96309400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
4	chr10:96306400-96309600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr10:96306400-96314200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:96306400-96314400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:96306400-96321200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:96306400-96325400	Weak transcription	Lung	lung
9	chr10:96306400-96330600	Weak transcription	Placenta	Placenta
10	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
12	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr10:96306400-96371000	Weak transcription	Ovary	ovary
15	chr10:96306600-96311600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:96306600-96314000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr10:96306600-96349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:96306600-96353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:96306800-96309000	Weak transcription	Fetal Heart	heart
21	chr10:96306800-96310200	Weak transcription	Fetal Intestine Small	intestine
22	chr10:96306800-96314200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr10:96306800-96314200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:96306800-96314400	Weak transcription	Fetal Muscle Leg	muscle
25	chr10:96306800-96314600	Weak transcription	Thymus	Thymus
26	chr10:96306800-96315800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:96306800-96317200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:96306800-96317200	Weak transcription	Fetal Intestine Large	intestine
29	chr10:96306800-96318600	Weak transcription	HSMM	muscle
30	chr10:96306800-96323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:96306800-96330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr10:96306800-96348000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr10:96306800-96348200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr10:96306800-96348400	Weak transcription	Primary B cells from cord blood	blood
35	chr10:96306800-96349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
38	chr10:96307000-96310000	Weak transcription	Fetal Stomach	stomach
39	chr10:96307000-96310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr10:96307000-96312400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:96307000-96314400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:96307000-96314800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:96307000-96358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:96307000-96375000	Weak transcription	Osteobl	bone
45	chr10:96307200-96310400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr10:96307200-96314000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:96307200-96314800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:96307200-96315000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr10:96307200-96315800	Weak transcription	NH-A	brain
50	chr10:96307200-96318600	Weak transcription	Muscle Satellite Cultured Cells	--

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