Variant report

Variant	rs12615367
Chromosome Location	chr2:178387547-178387548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178374449..178377274-chr2:178385680..178388103,2	K562	blood:
2	chr2:178385225..178387645-chr2:178388374..178391242,2	K562	blood:
3	chr2:178378596..178381431-chr2:178386070..178388398,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10170546	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10170667	0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10194648	0.81[ASN][1000 genomes]
rs10201153	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs10497500	0.85[JPT][hapmap]
rs10497501	0.82[JPT][hapmap]
rs10497502	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10497503	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10497508	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs10930792	0.80[ASN][1000 genomes]
rs12469386	0.85[JPT][hapmap]
rs12612857	0.86[JPT][hapmap]
rs12616093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618139	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs12990729	0.80[ASN][1000 genomes]
rs13000048	0.85[JPT][hapmap]
rs13004955	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1348848	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1348849	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1348850	0.95[JPT][hapmap]
rs1374437	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1405713	0.86[JPT][hapmap]
rs1453370	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1548067	0.86[JPT][hapmap]
rs16865203	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs16865216	0.89[ASN][1000 genomes]
rs16865229	0.89[ASN][1000 genomes]
rs16865291	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs16865328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16865331	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1901825	0.84[JPT][hapmap]
rs1901826	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1979058	0.80[ASN][1000 genomes]
rs2034678	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2060929	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2084233	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2121430	0.85[JPT][hapmap]
rs2166558	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2197611	0.81[ASN][1000 genomes]
rs2364853	0.90[ASN][1000 genomes]
rs2364854	0.85[JPT][hapmap]
rs3213945	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769995	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3769996	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.92[ASN][1000 genomes]
rs3769997	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3770002	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs3813259	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3902850	0.80[ASN][1000 genomes]
rs4243388	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4528793	0.86[JPT][hapmap]
rs4893821	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4893822	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4893823	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4893825	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4893935	0.85[JPT][hapmap]
rs4893936	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs4893950	0.84[JPT][hapmap]
rs4893951	0.87[ASN][1000 genomes]
rs4893957	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4893959	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4893961	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4893962	0.95[JPT][hapmap]
rs4893965	0.86[JPT][hapmap]
rs56942680	0.84[ASN][1000 genomes]
rs57273542	0.88[ASN][1000 genomes]
rs57295810	0.92[ASN][1000 genomes]
rs57527255	0.91[ASN][1000 genomes]
rs57541536	0.91[ASN][1000 genomes]
rs57733896	0.92[ASN][1000 genomes]
rs57948641	0.91[ASN][1000 genomes]
rs58297927	0.91[ASN][1000 genomes]
rs58483300	0.84[ASN][1000 genomes]
rs59111239	0.89[ASN][1000 genomes]
rs59421055	0.94[ASN][1000 genomes]
rs59504156	0.90[ASN][1000 genomes]
rs60642012	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60670838	0.89[ASN][1000 genomes]
rs60733259	0.84[ASN][1000 genomes]
rs6433670	0.81[ASN][1000 genomes]
rs6433673	0.82[ASN][1000 genomes]
rs6710575	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6742951	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7587604	0.85[JPT][hapmap]
rs7591807	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7604673	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7606235	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7607450	0.81[ASN][1000 genomes]
rs8941	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs952746	0.85[JPT][hapmap]
rs9679607	0.80[ASN][1000 genomes]
rs9789582	0.80[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12615367	LOC100130691	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:178331400-178388400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:178331800-178389400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:178332000-178392800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:178332000-178393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:178335000-178410600	Weak transcription	Thymus	Thymus
7	chr2:178338000-178403000	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:178339800-178394400	Weak transcription	Hela-S3	cervix
9	chr2:178342400-178392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:178342600-178391000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:178343800-178391200	Weak transcription	HMEC	breast
12	chr2:178348400-178402600	Weak transcription	NHDF-Ad	bronchial
13	chr2:178349800-178407800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:178350000-178407000	Weak transcription	Osteobl	bone
15	chr2:178354600-178392000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:178356000-178405400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:178358400-178390000	Weak transcription	Colonic Mucosa	Colon
18	chr2:178358600-178388400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:178358600-178406000	Weak transcription	Ovary	ovary
20	chr2:178358600-178417000	Weak transcription	Aorta	Aorta
21	chr2:178358800-178388600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:178358800-178396600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:178360600-178405400	Weak transcription	NH-A	brain
24	chr2:178362400-178395600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:178363000-178395600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:178364400-178416600	Weak transcription	Esophagus	oesophagus
27	chr2:178367800-178397200	Weak transcription	Psoas Muscle	Psoas
28	chr2:178370200-178391200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:178371000-178388400	Weak transcription	Small Intestine	intestine
30	chr2:178371400-178399800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:178372600-178405400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:178372800-178399200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:178372800-178416600	Weak transcription	A549	lung
34	chr2:178374400-178394400	Strong transcription	HepG2	liver
35	chr2:178375200-178400800	Weak transcription	Lung	lung
36	chr2:178375400-178394400	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:178375600-178413800	Weak transcription	K562	blood
38	chr2:178376000-178390600	Weak transcription	Fetal Brain Female	brain
39	chr2:178376000-178397400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:178376200-178407800	Weak transcription	Left Ventricle	heart
41	chr2:178376200-178416600	Weak transcription	Pancreas	Pancrea
42	chr2:178376600-178407600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:178378400-178410000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:178379600-178407600	Weak transcription	Fetal Kidney	kidney
45	chr2:178379800-178406000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:178380000-178388200	Weak transcription	Adipose Nuclei	Adipose
47	chr2:178380400-178390800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:178380400-178392600	Weak transcription	NHEK	skin
49	chr2:178380800-178391200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:178381600-178387600	Weak transcription	HSMM	muscle

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