Variant report

Variant	rs12703799
Chromosome Location	chr7:140070378-140070379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10235190	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11763598	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12667471	0.88[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12669654	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12703793	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12703794	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12703796	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341086	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4368896	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4448174	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4587251	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62490397	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62490398	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6464710	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6464713	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6953541	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6970664	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6976805	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7786963	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7796411	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7803606	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12703799	OR9A2	cis	cerebellum	SCAN
rs12703799	ZC3HAV1L	cis	parietal	SCAN
rs12703799	NDUFB2	cis	cerebellum	SCAN
rs12703799	TRIM2	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
3	chr7:140035000-140074200	Weak transcription	Right Atrium	heart
4	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
5	chr7:140046000-140076200	Weak transcription	Right Ventricle	heart
6	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
7	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:140049600-140076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
12	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
13	chr7:140051600-140076400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr7:140052600-140075600	Weak transcription	Pancreas	Pancrea
16	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
17	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
19	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:140055600-140079200	Weak transcription	Fetal Kidney	kidney
21	chr7:140056800-140077400	Weak transcription	NH-A	brain
22	chr7:140056800-140079400	Weak transcription	Colonic Mucosa	Colon
23	chr7:140057400-140075400	Weak transcription	Osteobl	bone
24	chr7:140058600-140075400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:140058600-140075600	Weak transcription	HepG2	liver
26	chr7:140058600-140077800	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
28	chr7:140058800-140075600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr7:140058800-140075600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:140058800-140075600	Weak transcription	Aorta	Aorta
31	chr7:140058800-140077800	Weak transcription	Placenta	Placenta
32	chr7:140058800-140079200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:140058800-140081400	Weak transcription	A549	lung
34	chr7:140058800-140084400	Weak transcription	Gastric	stomach
35	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
36	chr7:140059400-140075400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:140059400-140091400	Weak transcription	Fetal Heart	heart
38	chr7:140059600-140075600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr7:140059600-140075600	Weak transcription	NHLF	lung
40	chr7:140060000-140075600	Weak transcription	GM12878-XiMat	blood
41	chr7:140060200-140075600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:140060800-140074400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:140061000-140075600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:140061000-140076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:140063400-140082600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:140064600-140075200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:140064800-140075600	Weak transcription	Fetal Lung	lung
48	chr7:140065000-140075600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:140065000-140077000	Weak transcription	HMEC	breast
50	chr7:140065000-140077800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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