Variant report

Variant	rs3181362
Chromosome Location	chr9:117667443-117667444
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	REST	chr9:117667361-117667814	H1-neurons	neurons:	n/a	n/a
2	REST	chr9:117667190-117668097	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr9:117667374-117667955	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117659568..117662536-chr9:117667322..117669249,2	K562	blood:

Variant related genes	Relation type
TNFSF8	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10817681	0.97[AFR][1000 genomes]
rs10982448	0.85[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs16931962	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1885383	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2181032	0.90[ASN][1000 genomes]
rs3181192	1.00[TSI][hapmap]
rs3181194	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181346	0.94[ASW][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs3181349	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs3181350	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs3181357	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3181359	0.90[AFR][1000 genomes]
rs3181360	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789882	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3827818	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.99[ASN][1000 genomes]
rs4978612	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61024439	0.90[AFR][1000 genomes]
rs6478118	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7854103	0.90[AFR][1000 genomes]
rs7868670	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7871914	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs973351	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3181362	SPRED2	trans	brain	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117657800-117669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:117658600-117669200	Weak transcription	Fetal Stomach	stomach
3	chr9:117661800-117669800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:117662200-117676200	Weak transcription	Gastric	stomach
5	chr9:117662800-117670600	Weak transcription	Esophagus	oesophagus
6	chr9:117663000-117668600	Weak transcription	Placenta	Placenta
7	chr9:117663000-117669200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:117663200-117669000	Strong transcription	Primary B cells from cord blood	blood
9	chr9:117663400-117672800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:117663600-117668200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:117663600-117669000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr9:117663600-117672400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr9:117664000-117670200	Weak transcription	HSMMtube	muscle
14	chr9:117664400-117667800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:117664400-117668200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr9:117664400-117670200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:117664600-117668600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:117664800-117669200	Strong transcription	Thymus	Thymus
19	chr9:117665400-117668600	Weak transcription	HUVEC	blood vessel
20	chr9:117665400-117670200	Weak transcription	Osteobl	bone
21	chr9:117665400-117670400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:117665600-117667600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr9:117665600-117669200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:117665600-117669400	Weak transcription	HSMM	muscle
25	chr9:117665600-117671000	Weak transcription	NHLF	lung
26	chr9:117665800-117667600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:117665800-117667600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:117665800-117668800	Strong transcription	Primary T cells from cord blood	blood
29	chr9:117665800-117668800	Weak transcription	HMEC	breast
30	chr9:117665800-117669200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:117665800-117669200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:117665800-117669200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr9:117665800-117669200	Weak transcription	Small Intestine	intestine
34	chr9:117665800-117669400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:117665800-117669400	Weak transcription	Hela-S3	cervix
36	chr9:117665800-117669400	Weak transcription	NHEK	skin
37	chr9:117665800-117669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:117665800-117670400	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr9:117665800-117670400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:117665800-117672800	Weak transcription	Spleen	Spleen
41	chr9:117666000-117668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:117666000-117668600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:117666000-117668800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:117666000-117669200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:117666000-117669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:117666200-117667600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:117666400-117669200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:117666600-117667800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:117666600-117668600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:117666600-117669200	Weak transcription	Fetal Thymus	thymus

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