Variant report

Variant	rs2287512
Chromosome Location	chr2:53898032-53898033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10181876	0.88[EUR][1000 genomes]
rs10187718	0.83[EUR][1000 genomes]
rs10190578	0.87[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs10191950	0.84[EUR][1000 genomes]
rs10200897	0.87[EUR][1000 genomes]
rs10211188	0.82[EUR][1000 genomes]
rs10211650	0.88[EUR][1000 genomes]
rs11684574	0.81[ASN][1000 genomes]
rs12612895	0.91[ASN][1000 genomes]
rs12614610	0.91[ASN][1000 genomes]
rs12617315	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12618833	0.82[ASN][1000 genomes]
rs12620325	0.86[EUR][1000 genomes]
rs12621547	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12621635	0.90[CHD][hapmap];0.85[GIH][hapmap]
rs13414183	0.90[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs13414472	0.84[EUR][1000 genomes]
rs13423576	0.84[EUR][1000 genomes]
rs17045114	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17045116	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058953	0.92[ASN][1000 genomes]
rs2287344	0.81[CHD][hapmap]
rs2357491	0.92[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2357492	0.91[ASN][1000 genomes]
rs35833242	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3755120	0.84[CHD][hapmap]
rs3770398	0.87[EUR][1000 genomes]
rs3770400	0.88[EUR][1000 genomes]
rs3770401	0.87[CHD][hapmap];0.86[GIH][hapmap]
rs3770410	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3770412	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770415	0.92[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3821080	0.87[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4361164	0.90[ASN][1000 genomes]
rs56189833	0.86[ASN][1000 genomes]
rs66684820	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6705484	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs67073722	0.92[ASN][1000 genomes]
rs6712204	0.81[CHD][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap]
rs6714424	0.90[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs6716301	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717642	0.84[EUR][1000 genomes]
rs6760101	0.86[ASN][1000 genomes]
rs68123661	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs72793658	0.88[EUR][1000 genomes]
rs7582542	0.90[EUR][1000 genomes]
rs7586686	0.87[CHD][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap]
rs7595816	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs7609067	0.90[EUR][1000 genomes]
rs991599	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs994484	0.95[ASN][1000 genomes]
rs997644	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2287512	ASB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
5	chr2:53887800-53899800	Weak transcription	Primary B cells from cord blood	blood
6	chr2:53888200-53934200	Weak transcription	Lung	lung
7	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
8	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
9	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:53891600-53900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:53892600-53902600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart
13	chr2:53893400-53915200	Weak transcription	Ovary	ovary
14	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:53894200-53920800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:53894400-53900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:53894400-53912200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:53894400-53914400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:53894400-53925000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:53894600-53900000	Weak transcription	Stomach Mucosa	stomach
22	chr2:53894600-53911200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:53894800-53900000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:53895000-53900200	Weak transcription	Brain Substantia Nigra	brain
25	chr2:53895000-53911800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:53895400-53898600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:53895400-53919000	Weak transcription	Fetal Intestine Large	intestine
28	chr2:53895400-53921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:53895400-53925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:53895400-53926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:53895600-53914800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:53895600-53921400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:53895800-53916800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:53895800-53926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:53896000-53898200	Strong transcription	Primary T cells from cord blood	blood
36	chr2:53896000-53899400	Weak transcription	GM12878-XiMat	blood
37	chr2:53896000-53900000	Weak transcription	HSMM	muscle
38	chr2:53896000-53913000	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:53896000-53918800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:53896200-53911200	Weak transcription	Liver	Liver
41	chr2:53896200-53918400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:53896400-53926000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:53896600-53899600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:53896600-53900000	Weak transcription	Fetal Heart	heart
45	chr2:53896800-53898200	Enhancers	NHLF	lung
46	chr2:53896800-53900200	Weak transcription	NH-A	brain
47	chr2:53896800-53910200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:53896800-53910800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:53896800-53918800	Weak transcription	Fetal Brain Female	brain
50	chr2:53896800-53924800	Weak transcription	Thymus	Thymus

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