Variant report

Variant	rs12351083
Chromosome Location	chr9:117775768-117775769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117443499..117444975-chr9:117775722..117777924,20	MCF-7	breast:
2	chr9:117770232..117771827-chr9:117773416..117775820,2	K562	blood:
3	chr9:117442900..117446108-chr9:117775232..117777695,3	MCF-7	breast:
4	chr9:117660650..117663296-chr9:117774626..117776386,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10817700	0.89[ASN][1000 genomes]
rs10817701	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10982497	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10982503	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10982504	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10982509	0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs11788513	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11792749	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs12343737	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs12344929	0.82[YRI][hapmap]
rs12346540	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12347433	0.86[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12348090	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.82[YRI][hapmap]
rs12349585	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap]
rs13286217	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1411453	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs1411455	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs2274835	0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2297179	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.82[YRI][hapmap]
rs2297181	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs34690752	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789871	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.82[YRI][hapmap]
rs3789875	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4452883	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7859478	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12351083	TNFSF8	cis	parietal	SCAN
rs12351083	TXN	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117768400-117776000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:117769800-117775800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:117771200-117783000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:117771400-117776200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr9:117771400-117778600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:117771400-117784600	Weak transcription	HMEC	breast
7	chr9:117771600-117776000	Weak transcription	Hela-S3	cervix
8	chr9:117771800-117779000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:117772600-117775800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:117773000-117776000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
12	chr9:117773600-117776000	Weak transcription	Fetal Lung	lung
13	chr9:117773600-117787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:117773800-117776600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:117774200-117775800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr9:117774200-117776200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:117774400-117780400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:117774800-117783200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:117775000-117782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:117775200-117777000	Enhancers	Dnd41	blood
21	chr9:117775600-117780400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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