Variant report

Variant	rs7039716
Chromosome Location	chr9:102670215-102670216
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:102668649-102670376	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:102668488-102670759	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:102668911-102670682	K562	blood:	n/a	n/a
4	POLR2A	chr9:102670148-102670428	MCF-7	breast:	n/a	n/a

No data

(count:10 , 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	chr9:102670054..102672961-chr9:102682119..102683745,2	MCF-7	breast:
5	chr9:102668724..102670876-chr9:102691785..102694126,2	MCF-7	breast:
6	chr9:102668815..102670753-chr9:102697540..102700821,3	K562	blood:
7	chr9:102668815..102670753-chr9:102698922..102700821,2	K562	blood:
8	chr9:101982798..101985464-chr9:102669885..102671484,2	MCF-7	breast:
9	chr9:102667836..102670748-chr9:102860445..102862735,2	K562	blood:
10	chr9:102580482..102589062-chr9:102666380..102672134,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255145	TF binding region
ENSG00000136874	Chromatin interaction
ENSG00000119523	Chromatin interaction
ENSG00000254571	Chromatin interaction
ENSG00000119508	Chromatin interaction
ENSG00000237461	Chromatin interaction
ENSG00000106803	Chromatin interaction
ENSG00000119509	Chromatin interaction
ENSG00000023318	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10116142	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10117638	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10117828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118565	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10120103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122128	0.93[ASN][1000 genomes]
rs10123261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124366	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10125981	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10217337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217366	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739791	0.93[ASN][1000 genomes]
rs10739792	0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs10739793	0.93[ASN][1000 genomes]
rs10739794	0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs10760698	0.92[ASN][1000 genomes]
rs10760699	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760705	0.92[ASN][1000 genomes]
rs10760706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819705	0.92[ASN][1000 genomes]
rs10819706	0.93[ASN][1000 genomes]
rs10819707	0.93[ASN][1000 genomes]
rs10819711	0.93[ASN][1000 genomes]
rs10819712	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs10988919	0.93[ASN][1000 genomes]
rs10988920	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988945	0.84[YRI][hapmap]
rs10988973	0.87[YRI][hapmap]
rs12352899	0.93[ASN][1000 genomes]
rs1342147	0.87[YRI][hapmap]
rs1361668	0.88[YRI][hapmap]
rs1529191	0.82[YRI][hapmap]
rs16918878	0.88[JPT][hapmap]
rs1830454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881751	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1962051	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1969577	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1997367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031035	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181579	0.82[YRI][hapmap]
rs2416935	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]
rs2416936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2416937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416938	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416941	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416942	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2698999	0.83[YRI][hapmap]
rs2795575	0.83[YRI][hapmap]
rs2900224	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739794	0.93[ASN][1000 genomes]
rs3983846	0.92[ASN][1000 genomes]
rs4282626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517187	0.87[YRI][hapmap]
rs4585797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742779	0.83[YRI][hapmap]
rs4743370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478987	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478988	0.92[ASN][1000 genomes]
rs6478990	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022208	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7022999	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030388	0.94[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs7038506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853264	0.93[ASN][1000 genomes]
rs9299335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9556	0.96[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7039716	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102668200-102670400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:102668400-102670400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:102668400-102670400	Active TSS	Fetal Intestine Large	intestine
4	chr9:102668600-102670600	Active TSS	Brain Anterior Caudate	brain
5	chr9:102669400-102670400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:102669600-102670400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:102669600-102670400	Flanking Active TSS	Dnd41	blood
8	chr9:102669600-102670600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:102669600-102681200	Weak transcription	Spleen	Spleen
10	chr9:102669800-102670400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:102669800-102670400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr9:102669800-102670400	Weak transcription	Thymus	Thymus
13	chr9:102669800-102671200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:102669800-102671200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr9:102669800-102671200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr9:102669800-102671600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr9:102669800-102677400	Weak transcription	Placenta	Placenta
18	chr9:102669800-102677800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:102669800-102677800	Weak transcription	Esophagus	oesophagus
20	chr9:102669800-102677800	Weak transcription	Left Ventricle	heart
21	chr9:102669800-102678000	Weak transcription	Ovary	ovary
22	chr9:102669800-102678200	Weak transcription	Brain Substantia Nigra	brain
23	chr9:102669800-102678200	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:102669800-102679800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:102669800-102680200	Weak transcription	Aorta	Aorta
26	chr9:102669800-102680200	Weak transcription	Gastric	stomach
27	chr9:102669800-102680200	Weak transcription	Lung	lung
28	chr9:102669800-102680200	Weak transcription	Pancreas	Pancrea
29	chr9:102669800-102681200	Weak transcription	Colonic Mucosa	Colon
30	chr9:102669800-102682400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:102669800-102684600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:102669800-102684800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:102669800-102686000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:102669800-102686200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:102669800-102687600	Weak transcription	Stomach Mucosa	stomach
36	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
37	chr9:102670000-102670400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:102670000-102670400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr9:102670000-102670400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr9:102670000-102670400	Enhancers	Primary B cells from peripheral blood	blood
41	chr9:102670000-102670400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:102670000-102670400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr9:102670000-102670400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr9:102670000-102670400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:102670000-102670400	Flanking Active TSS	Liver	Liver
46	chr9:102670000-102670400	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:102670000-102670400	Enhancers	Rectal Smooth Muscle	rectum
48	chr9:102670000-102670400	Flanking Active TSS	GM12878-XiMat	blood
49	chr9:102670000-102670400	Enhancers	HUVEC	blood vessel
50	chr9:102670000-102670400	Enhancers	Monocytes-CD14+_RO01746	blood

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