Variant report

Variant	rs10982497
Chromosome Location	chr9:117785048-117785049
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117779697..117782245-chr9:117783461..117785419,2	K562	blood:
2	chr9:117779444..117782245-chr9:117782697..117785419,3	K562	blood:
3	chr9:117158967..117160760-chr9:117784217..117787013,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10817700	0.83[ASN][1000 genomes]
rs10817701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10982503	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982504	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982509	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs11788513	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11792749	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs12343737	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12346540	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12347433	0.86[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12348090	0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap]
rs12349585	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap]
rs12351083	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13286217	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1411453	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1411455	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs2274835	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2297179	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap]
rs2297181	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs34690752	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789871	0.90[JPT][hapmap];1.00[LWK][hapmap]
rs3789875	0.86[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4452883	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7859478	0.81[CHB][hapmap];0.90[JPT][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
rs10982497	TXN	cis	cerebellum	SCAN
rs10982497	TNFSF8	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117773600-117787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:117776400-117786000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:117776800-117791600	Weak transcription	Fetal Lung	lung
5	chr9:117779800-117787600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:117781000-117788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:117781800-117791600	Weak transcription	Aorta	Aorta
8	chr9:117781800-117797400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:117781800-117798200	Weak transcription	Fetal Intestine Large	intestine
10	chr9:117781800-117798400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:117782000-117785400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:117782000-117788200	Weak transcription	Spleen	Spleen
14	chr9:117782000-117789600	Weak transcription	Gastric	stomach
15	chr9:117782200-117785400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:117782200-117786000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:117782200-117786600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
19	chr9:117782600-117785400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:117783000-117785200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:117783000-117787200	Strong transcription	Colon Smooth Muscle	Colon
22	chr9:117783000-117787400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:117783200-117785600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:117783200-117785600	Strong transcription	NHEK	skin
25	chr9:117783200-117786800	Strong transcription	Fetal Muscle Leg	muscle
26	chr9:117783200-117789000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:117783200-117790000	Strong transcription	Fetal Stomach	stomach
28	chr9:117783200-117792400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:117783200-117796800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:117783400-117785200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:117783800-117785600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr9:117784000-117785400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:117784200-117786800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr9:117784200-117787400	Genic enhancers	NHDF-Ad	bronchial
35	chr9:117784400-117786600	Genic enhancers	NHLF	lung
36	chr9:117784400-117788200	Genic enhancers	Osteobl	bone
37	chr9:117784400-117789000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:117784400-117790200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr9:117784400-117791600	Weak transcription	Fetal Kidney	kidney
40	chr9:117784600-117785400	Enhancers	HSMMtube	muscle
41	chr9:117784600-117786200	Enhancers	HSMM	muscle
42	chr9:117784600-117788000	Genic enhancers	NH-A	brain
43	chr9:117784600-117788200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:117784600-117788400	Enhancers	HMEC	breast
45	chr9:117784800-117785400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:117784800-117786000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr9:117784800-117786600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:117785000-117786200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:117785000-117786800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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