Variant report

Variant	rs6493882
Chromosome Location	chr15:57016382-57016383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10518871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852822	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11856432	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16977020	0.81[LWK][hapmap]
rs2128171	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28437201	0.85[EUR][1000 genomes]
rs3784553	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs59066195	0.84[ASN][1000 genomes]
rs6493886	0.94[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164095	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171500	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7172110	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7173137	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7175191	0.81[CEU][hapmap]
rs7181745	0.87[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6493882	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs6493882	TEX9	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
2	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:56992400-57021800	Weak transcription	Right Ventricle	heart
5	chr15:56992600-57022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:56993400-57021600	Weak transcription	Fetal Brain Male	brain
8	chr15:56994000-57023800	Weak transcription	Fetal Kidney	kidney
9	chr15:56995800-57022200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:56996000-57021800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:56996400-57021600	Weak transcription	HSMMtube	muscle
12	chr15:56996400-57022600	Weak transcription	NH-A	brain
13	chr15:56996800-57022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:56997200-57016400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:56997200-57016600	Weak transcription	Left Ventricle	heart
16	chr15:56997200-57022800	Weak transcription	Gastric	stomach
17	chr15:56997200-57023800	Weak transcription	Fetal Stomach	stomach
18	chr15:56998400-57021200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:56998800-57021800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:56998800-57023400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr15:56998800-57023800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:56999200-57017800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:56999400-57023400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:57008000-57017200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:57009200-57021400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:57009400-57022800	Weak transcription	Right Atrium	heart
27	chr15:57009400-57024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:57011000-57022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:57011200-57016400	Weak transcription	Brain Anterior Caudate	brain
30	chr15:57011200-57022600	Weak transcription	Fetal Heart	heart
31	chr15:57011400-57021200	Weak transcription	Brain Substantia Nigra	brain
32	chr15:57011400-57021400	Weak transcription	Adipose Nuclei	Adipose
33	chr15:57011400-57021800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:57011600-57016600	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:57011600-57018400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:57011600-57021000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:57011600-57022600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:57011600-57023400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:57011600-57024400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:57011600-57024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:57011800-57019200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:57011800-57022600	Weak transcription	HMEC	breast
43	chr15:57011800-57024000	Weak transcription	Aorta	Aorta
44	chr15:57012400-57022600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:57012400-57022600	Weak transcription	Osteobl	bone
46	chr15:57012400-57025000	Weak transcription	Spleen	Spleen
47	chr15:57012600-57017200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:57012600-57022600	Weak transcription	NHEK	skin
49	chr15:57012600-57023000	Weak transcription	NHLF	lung
50	chr15:57012600-57023400	Weak transcription	Psoas Muscle	Psoas

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