Variant report

Variant	rs1962051
Chromosome Location	chr9:102669877-102669878
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:102668889-102669880	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:102668649-102670376	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:102668488-102670759	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr9:102668911-102670682	K562	blood:	n/a	n/a
5	MXI1	chr9:102668917-102669878	GM12878	blood:	n/a	n/a
6	MAFK	chr9:102669849-102669888	Hela-S3	cervix:	n/a	n/a
7	WRNIP1	chr9:102669773-102669922	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:102580555..102587852-chr9:102667958..102670918,11	MCF-7	breast:
2	chr9:102580574..102584384-chr9:102666062..102670667,9	K562	blood:
3	chr9:102580667..102584355-chr9:102667685..102671328,3	K562	blood:
4	chr9:102668724..102670876-chr9:102691785..102694126,2	MCF-7	breast:
5	chr9:102668815..102670753-chr9:102697540..102700821,3	K562	blood:
6	chr9:102668815..102670753-chr9:102698922..102700821,2	K562	blood:
7	chr9:102667836..102670748-chr9:102860445..102862735,2	K562	blood:
8	chr9:102580482..102589062-chr9:102666380..102672134,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255145	TF binding region
ENSG00000237461	Chromatin interaction
ENSG00000023318	Chromatin interaction
ENSG00000119509	Chromatin interaction
ENSG00000136874	Chromatin interaction
ENSG00000119508	Chromatin interaction
ENSG00000254571	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10116142	0.83[JPT][hapmap]
rs10117638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117828	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10120103	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10121601	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10121880	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10122128	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123261	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10124366	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10125981	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217337	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10217366	0.93[ASN][1000 genomes]
rs10217692	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10512268	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1055187	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739791	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739793	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760698	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760700	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760704	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760705	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760706	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10819705	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819706	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819707	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819711	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988919	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988920	0.92[ASN][1000 genomes]
rs12352899	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830454	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1852863	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs1881751	0.90[ASN][1000 genomes]
rs1969577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997367	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1997368	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2031035	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs2416935	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416936	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2416937	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416938	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416940	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416941	0.93[ASN][1000 genomes]
rs2416942	0.93[ASN][1000 genomes]
rs2900224	0.92[ASN][1000 genomes]
rs3739794	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3983846	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282626	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4452862	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4585797	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742777	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742778	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743370	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6478987	0.93[ASN][1000 genomes]
rs6478988	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478990	0.93[ASN][1000 genomes]
rs7022208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022999	0.93[ASN][1000 genomes]
rs7027619	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7027813	0.95[ASN][1000 genomes]
rs7030388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038506	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7039716	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7853264	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299335	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]

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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	esv3366813	chr9:102657446-102670065	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1962051	STX17	Cis_1M	lymphoblastoid	RTeQTL
rs1962051	INVS	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102668200-102670000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:102668200-102670000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr9:102668200-102670000	Active TSS	Fetal Intestine Small	intestine
4	chr9:102668200-102670000	Active TSS	Fetal Kidney	kidney
5	chr9:102668200-102670000	Active TSS	HSMMtube	muscle
6	chr9:102668200-102670200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:102668200-102670200	Active TSS	NHDF-Ad	bronchial
8	chr9:102668200-102670400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr9:102668400-102670000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr9:102668400-102670000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:102668400-102670000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:102668400-102670000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:102668400-102670000	Active TSS	Fetal Brain Male	brain
14	chr9:102668400-102670000	Active TSS	Fetal Muscle Trunk	muscle
15	chr9:102668400-102670000	Active TSS	Right Atrium	heart
16	chr9:102668400-102670000	Active TSS	Right Ventricle	heart
17	chr9:102668400-102670000	Active TSS	NH-A	brain
18	chr9:102668400-102670200	Active TSS	NHLF	lung
19	chr9:102668400-102670400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:102668400-102670400	Active TSS	Fetal Intestine Large	intestine
21	chr9:102668600-102670000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr9:102668600-102670000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:102668600-102670000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:102668600-102670000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr9:102668600-102670000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr9:102668600-102670000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:102668600-102670000	Active TSS	Brain Cingulate Gyrus	brain
28	chr9:102668600-102670000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:102668600-102670000	Active TSS	Fetal Stomach	stomach
30	chr9:102668600-102670000	Active TSS	Psoas Muscle	Psoas
31	chr9:102668600-102670000	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr9:102668600-102670000	Active TSS	Stomach Smooth Muscle	stomach
33	chr9:102668600-102670200	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr9:102668600-102670200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:102668600-102670200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr9:102668600-102670200	Active TSS	A549	lung
37	chr9:102668600-102670200	Active TSS	HepG2	liver
38	chr9:102668600-102670600	Active TSS	Brain Anterior Caudate	brain
39	chr9:102668800-102670000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:102668800-102670000	Active TSS	Liver	Liver
41	chr9:102668800-102670000	Active TSS	Fetal Thymus	thymus
42	chr9:102668800-102670000	Active TSS	NHEK	skin
43	chr9:102668800-102670200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr9:102668800-102670200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:102668800-102670200	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr9:102668800-102670200	Active TSS	HMEC	breast
47	chr9:102668800-102670200	Active TSS	K562	blood
48	chr9:102669400-102670000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr9:102669400-102670000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr9:102669400-102670000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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