Variant report

Variant	rs10124366
Chromosome Location	chr9:102687703-102687704
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	KAP1	chr9:102687496-102688678	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:102685655..102688610-chr9:102689840..102691723,2	MCF-7	breast:
2	chr9:102681063..102683683-chr9:102683801..102687863,4	MCF-7	breast:
3	chr9:102687179..102688964-chr9:102696441..102698384,2	K562	blood:
4	chr9:102679685..102682942-chr9:102684269..102688000,3	K562	blood:

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

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10116142	0.94[JPT][hapmap]
rs10117638	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs10117828	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10120103	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10121601	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10121880	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10122128	0.81[ASN][1000 genomes]
rs10123261	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10125981	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs10217337	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10217366	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10217692	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10512268	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10739791	0.81[ASN][1000 genomes]
rs10739792	0.81[ASN][1000 genomes]
rs10739793	0.81[ASN][1000 genomes]
rs10760699	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs10760700	0.81[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10760704	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10760706	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10819706	0.81[ASN][1000 genomes]
rs10819707	0.81[ASN][1000 genomes]
rs10819711	0.81[ASN][1000 genomes]
rs10819712	0.81[ASN][1000 genomes]
rs10988919	0.81[ASN][1000 genomes]
rs10988920	0.85[ASN][1000 genomes]
rs12352899	0.81[ASN][1000 genomes]
rs12684341	0.80[ASN][1000 genomes]
rs16918878	0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.81[YRI][hapmap]
rs1830454	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1852863	0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1881751	0.83[ASN][1000 genomes]
rs1962051	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs1969577	0.81[ASN][1000 genomes]
rs1997367	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1997368	0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2031035	0.81[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2416935	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2416936	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2416937	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2416938	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2416940	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2416941	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2416942	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2900224	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3739794	0.81[ASN][1000 genomes]
rs4282626	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4452862	0.87[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4585797	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4742777	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4742778	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4743370	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6478987	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6478990	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7022208	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs7022999	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7027619	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7027813	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7030388	0.81[ASN][1000 genomes]
rs7038506	0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7039716	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7853264	0.81[ASN][1000 genomes]
rs9299335	0.81[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9556	0.81[CHD][hapmap];0.87[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10124366	STX17	Cis_1M	lymphoblastoid	RTeQTL
rs10124366	STX17	cis	cerebellum	SCAN
rs10124366	C9orf125	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
2	chr9:102670000-102688200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:102670400-102688600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
5	chr9:102676600-102688000	Strong transcription	Primary B cells from cord blood	blood
6	chr9:102677600-102687800	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:102680000-102710800	Weak transcription	HUVEC	blood vessel
8	chr9:102680400-102693800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:102680400-102724800	Weak transcription	HSMM	muscle
10	chr9:102680600-102689000	Weak transcription	Fetal Brain Male	brain
11	chr9:102681800-102690400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:102682600-102693800	Weak transcription	Osteobl	bone
13	chr9:102682600-102751400	Weak transcription	NH-A	brain
14	chr9:102682800-102687800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:102682800-102695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:102683600-102687800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr9:102684200-102687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:102684200-102689400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:102684400-102691400	Weak transcription	NHDF-Ad	bronchial
20	chr9:102684400-102720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:102684600-102688200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:102684600-102693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:102684800-102687800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:102684800-102689800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:102685000-102687800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:102685000-102690800	Weak transcription	HSMMtube	muscle
27	chr9:102685000-102698200	Weak transcription	NHEK	skin
28	chr9:102685000-102710000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr9:102685200-102730200	Weak transcription	NHLF	lung
31	chr9:102685400-102690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:102685800-102689400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr9:102685800-102691000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:102685800-102698000	Weak transcription	HMEC	breast
35	chr9:102686000-102688800	Weak transcription	Left Ventricle	heart
36	chr9:102686000-102695400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr9:102686000-102699400	Weak transcription	K562	blood
38	chr9:102686200-102690800	Weak transcription	Brain Angular Gyrus	brain
39	chr9:102686200-102694400	Weak transcription	Brain Substantia Nigra	brain
40	chr9:102686200-102699200	Weak transcription	Fetal Kidney	kidney
41	chr9:102686200-102699400	Weak transcription	Psoas Muscle	Psoas
42	chr9:102686200-102730000	Weak transcription	Colonic Mucosa	Colon
43	chr9:102686400-102687800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:102686400-102687800	Weak transcription	Adipose Nuclei	Adipose
45	chr9:102686400-102687800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:102686400-102689000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:102686400-102689200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:102686400-102689200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:102686400-102693600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:102686400-102694600	Weak transcription	Brain Hippocampus Middle	brain

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