Variant report

Variant	rs17402964
Chromosome Location	chr3:101067945-101067946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11707689	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11710016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711808	0.93[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs12485950	0.87[JPT][hapmap]
rs12638137	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638796	0.90[EUR][1000 genomes]
rs2460723	0.81[JPT][hapmap]
rs348867	0.81[JPT][hapmap]
rs348877	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs348878	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs348882	0.81[JPT][hapmap]
rs348883	0.81[JPT][hapmap]
rs488679	0.81[JPT][hapmap]
rs518813	0.81[JPT][hapmap]
rs55710435	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56171035	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57880921	0.90[EUR][1000 genomes]
rs58835747	0.84[EUR][1000 genomes]
rs59359251	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72940399	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942211	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72944107	0.90[EUR][1000 genomes]
rs72946021	0.81[EUR][1000 genomes]
rs7613046	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9861403	0.84[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17402964	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101030800-101096400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:101038600-101101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:101038800-101089800	Weak transcription	Pancreas	Pancrea
4	chr3:101039800-101106600	Weak transcription	Thymus	Thymus
5	chr3:101040400-101070800	Weak transcription	NHDF-Ad	bronchial
6	chr3:101040600-101086800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:101040800-101076000	Weak transcription	Esophagus	oesophagus
8	chr3:101040800-101090000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:101042000-101069200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:101042200-101070800	Weak transcription	Osteobl	bone
11	chr3:101042800-101089600	Weak transcription	NH-A	brain
12	chr3:101043200-101076000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:101043200-101105000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:101043800-101096600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:101044400-101074200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:101044400-101103000	Weak transcription	Gastric	stomach
17	chr3:101044600-101076000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:101044600-101081800	Weak transcription	Aorta	Aorta
19	chr3:101044800-101079800	Weak transcription	Spleen	Spleen
20	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:101046400-101074200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:101046400-101076200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:101046400-101089000	Weak transcription	Fetal Brain Male	brain
24	chr3:101046800-101074200	Weak transcription	Fetal Brain Female	brain
25	chr3:101046800-101076000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:101046800-101076200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:101047000-101071200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:101047200-101076200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:101047400-101096000	Weak transcription	Psoas Muscle	Psoas
30	chr3:101047600-101073400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:101047800-101069000	Weak transcription	GM12878-XiMat	blood
32	chr3:101048400-101075800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:101048400-101076600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:101048400-101082400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:101048400-101084400	Weak transcription	HSMM	muscle
36	chr3:101048600-101088000	Weak transcription	HUVEC	blood vessel
37	chr3:101049200-101096000	Weak transcription	Ovary	ovary
38	chr3:101049200-101102200	Weak transcription	Right Ventricle	heart
39	chr3:101050400-101074400	Weak transcription	Left Ventricle	heart
40	chr3:101052600-101069200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:101052800-101068200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:101053200-101082600	Weak transcription	Fetal Stomach	stomach
43	chr3:101053200-101083200	Weak transcription	K562	blood
44	chr3:101054600-101085000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:101055800-101076000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:101056200-101076000	Weak transcription	Lung	lung
47	chr3:101056200-101081600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:101056200-101082600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:101056200-101082800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:101056200-101084600	Weak transcription	Fetal Heart	heart

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