Variant report

Variant	rs3768686
Chromosome Location	chr2:148692776-148692777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10180655	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10439198	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11686483	0.96[ASN][1000 genomes]
rs12105745	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1227304	0.96[ASN][1000 genomes]
rs1234416	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12622150	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12989087	0.91[ASN][1000 genomes]
rs13016893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13399553	0.88[EUR][1000 genomes]
rs13430086	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1895694	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs2113792	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2113794	0.93[ASN][1000 genomes]
rs2194695	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2303391	1.00[YRI][hapmap]
rs2603597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2603600	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2627019	0.94[ASN][1000 genomes]
rs2627025	0.93[ASN][1000 genomes]
rs3768684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768688	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3820716	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4419186	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55816333	0.91[ASN][1000 genomes]
rs56073268	0.91[ASN][1000 genomes]
rs6709182	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs6713811	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6731371	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7566230	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7582403	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs7593570	0.94[ASN][1000 genomes]
rs9287411	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875275	chr2:148166428-148711242	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv535969	chr2:148677122-148715921	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3768686	ACVR2A	cis	cerebellum	SCAN
rs3768686	ORC4L	Cis_1M	lymphoblastoid	RTeQTL
rs3768686	MMADHC	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148647200-148719600	Weak transcription	Pancreas	Pancrea
3	chr2:148650200-148719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:148652800-148693600	Weak transcription	Lung	lung
5	chr2:148653200-148719600	Weak transcription	Esophagus	oesophagus
6	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
7	chr2:148659600-148719800	Weak transcription	Gastric	stomach
8	chr2:148661600-148718200	Weak transcription	Fetal Intestine Small	intestine
9	chr2:148664600-148721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:148664800-148693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:148671800-148698800	Weak transcription	NHEK	skin
12	chr2:148671800-148719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:148672000-148692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:148672000-148693000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:148672200-148693800	Weak transcription	HUVEC	blood vessel
16	chr2:148672200-148695800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:148672200-148706800	Weak transcription	Brain Germinal Matrix	brain
18	chr2:148672400-148692800	Weak transcription	Stomach Mucosa	stomach
19	chr2:148675400-148708800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:148676200-148722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:148676600-148693600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:148677200-148696200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:148678000-148718200	Weak transcription	Right Ventricle	heart
24	chr2:148679000-148718800	Weak transcription	Fetal Stomach	stomach
25	chr2:148679600-148737200	Weak transcription	Hela-S3	cervix
26	chr2:148681000-148729600	Weak transcription	NHDF-Ad	bronchial
27	chr2:148683000-148708400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:148683000-148725200	Weak transcription	Fetal Heart	heart
29	chr2:148683200-148708800	Weak transcription	Psoas Muscle	Psoas
30	chr2:148685000-148707600	Weak transcription	Fetal Brain Male	brain
31	chr2:148685000-148708600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:148685200-148701200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:148685200-148707400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:148686200-148693000	Weak transcription	Brain Angular Gyrus	brain
35	chr2:148686400-148695200	Weak transcription	K562	blood
36	chr2:148688200-148702600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:148688200-148719800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:148688200-148728600	Weak transcription	NH-A	brain
39	chr2:148688400-148707400	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:148688800-148708600	Weak transcription	GM12878-XiMat	blood
41	chr2:148688800-148719600	Weak transcription	Thymus	Thymus
42	chr2:148689000-148701800	Weak transcription	Colonic Mucosa	Colon
43	chr2:148689200-148693600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:148689200-148708600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:148690000-148693400	Strong transcription	Fetal Lung	lung
46	chr2:148690000-148694000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:148690000-148694000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:148690000-148694000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:148690000-148694000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr2:148690000-148694000	Strong transcription	A549	lung

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