Variant report

Variant	rs10117828
Chromosome Location	chr9:102688717-102688718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr9:102688531-102688731	HepG2	liver:	n/a	n/a
2	MAFK	chr9:102688603-102688767	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102667945..102670495-chr9:102688476..102690798,2	K562	blood:
2	chr9:102687179..102688964-chr9:102696441..102698384,2	K562	blood:

Variant related genes	Relation type
STX17	TF binding region
ENSG00000136874	Chromatin interaction
ENSG00000255145	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10116142	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs10117638	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10118565	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10120103	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]
rs10121601	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];0.98[ASN][1000 genomes]
rs10121880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124366	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217692	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988945	0.88[YRI][hapmap]
rs10988973	0.82[YRI][hapmap]
rs12352899	0.93[ASN][1000 genomes]
rs1342147	0.82[YRI][hapmap]
rs1361668	0.84[YRI][hapmap]
rs1539297	0.84[YRI][hapmap]
rs16918878	0.88[JPT][hapmap]
rs1830454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881751	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031035	0.95[CEU][hapmap];1.00[CHB][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]
rs2416935	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]
rs2416936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2416937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416938	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs2416940	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]
rs2416941	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2698999	0.87[YRI][hapmap]
rs2795575	0.87[YRI][hapmap]
rs2900224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452862	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517187	0.82[YRI][hapmap]
rs4585797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742778	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]
rs4743370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478988	0.92[ASN][1000 genomes]
rs6478990	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022208	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7022999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027619	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]
rs7027813	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039716	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]
rs7853264	0.93[ASN][1000 genomes]
rs846759	0.84[YRI][hapmap]
rs9299335	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]
rs9556	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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	nsv1050510	chr9:102684318-102748658	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10117828	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
2	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
3	chr9:102680000-102710800	Weak transcription	HUVEC	blood vessel
4	chr9:102680400-102693800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:102680400-102724800	Weak transcription	HSMM	muscle
6	chr9:102680600-102689000	Weak transcription	Fetal Brain Male	brain
7	chr9:102681800-102690400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:102682600-102693800	Weak transcription	Osteobl	bone
9	chr9:102682600-102751400	Weak transcription	NH-A	brain
10	chr9:102682800-102695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:102684200-102689400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:102684400-102691400	Weak transcription	NHDF-Ad	bronchial
13	chr9:102684400-102720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:102684600-102693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:102684800-102689800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:102685000-102690800	Weak transcription	HSMMtube	muscle
17	chr9:102685000-102698200	Weak transcription	NHEK	skin
18	chr9:102685000-102710000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:102685200-102730200	Weak transcription	NHLF	lung
21	chr9:102685400-102690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:102685800-102689400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr9:102685800-102691000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:102685800-102698000	Weak transcription	HMEC	breast
25	chr9:102686000-102688800	Weak transcription	Left Ventricle	heart
26	chr9:102686000-102695400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:102686000-102699400	Weak transcription	K562	blood
28	chr9:102686200-102690800	Weak transcription	Brain Angular Gyrus	brain
29	chr9:102686200-102694400	Weak transcription	Brain Substantia Nigra	brain
30	chr9:102686200-102699200	Weak transcription	Fetal Kidney	kidney
31	chr9:102686200-102699400	Weak transcription	Psoas Muscle	Psoas
32	chr9:102686200-102730000	Weak transcription	Colonic Mucosa	Colon
33	chr9:102686400-102689000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:102686400-102689200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:102686400-102689200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:102686400-102693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:102686400-102694600	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:102686400-102694600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:102686400-102699400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:102686400-102712800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:102686400-102713000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:102686400-102723400	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:102686400-102750800	Weak transcription	Esophagus	oesophagus
44	chr9:102686600-102688800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:102686600-102688800	Weak transcription	Fetal Stomach	stomach
46	chr9:102686600-102688800	Weak transcription	Fetal Thymus	thymus
47	chr9:102686600-102688800	Weak transcription	Lung	lung
48	chr9:102686600-102689200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:102686600-102690400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:102686600-102690600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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