Variant report

Variant	rs2627019
Chromosome Location	chr2:148729050-148729051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10180655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10439198	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10439199	0.80[EUR][1000 genomes]
rs10928375	0.80[EUR][1000 genomes]
rs11686483	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12105745	0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1227304	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234396	0.84[ASN][1000 genomes]
rs1234397	0.84[ASN][1000 genomes]
rs1234416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1234418	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1234430	0.80[EUR][1000 genomes]
rs12622150	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12989087	0.85[ASN][1000 genomes]
rs13016893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430086	0.82[CEU][hapmap];0.93[ASN][1000 genomes]
rs1872198	0.84[ASN][1000 genomes]
rs1895694	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2100469	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2113792	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2113794	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2194695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288190	0.81[YRI][hapmap]
rs2382202	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2603597	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603599	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2603600	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2627025	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768684	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768686	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3768688	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3820716	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4419186	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55816333	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56073268	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6709182	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs6713811	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6731371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7566230	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7577025	0.84[ASN][1000 genomes]
rs7582403	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7593570	1.00[ASN][1000 genomes]
rs9287411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs979636	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1004169	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv535970	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv869326	chr2:148727068-148859804	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2627019	ORC4L	Cis_1M	lymphoblastoid	RTeQTL
rs2627019	ACVR2A	cis	parietal	SCAN

Chromatin state (count:103 , 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	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
3	chr2:148679600-148737200	Weak transcription	Hela-S3	cervix
4	chr2:148681000-148729600	Weak transcription	NHDF-Ad	bronchial
5	chr2:148691000-148734600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:148694000-148731400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:148694200-148777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:148694400-148738400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:148694400-148741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:148694400-148741200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:148694600-148731600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:148695000-148746800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:148698000-148734000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:148701000-148730200	Weak transcription	Placenta	Placenta
15	chr2:148707600-148732200	Weak transcription	Stomach Mucosa	stomach
16	chr2:148709000-148738400	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:148709200-148737800	Weak transcription	Fetal Brain Male	brain
18	chr2:148709200-148747600	Weak transcription	Adipose Nuclei	Adipose
19	chr2:148709400-148731800	Weak transcription	Left Ventricle	heart
20	chr2:148709400-148732000	Weak transcription	HUVEC	blood vessel
21	chr2:148709400-148735000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:148709400-148776800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:148709600-148741400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:148709800-148747000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:148713200-148729800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:148713600-148735000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:148715600-148734800	Weak transcription	HSMM	muscle
28	chr2:148715800-148729200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:148720000-148735600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:148720000-148736800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:148720600-148735200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:148720800-148741400	Weak transcription	Gastric	stomach
33	chr2:148721200-148735400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:148721200-148735400	Weak transcription	Pancreas	Pancrea
35	chr2:148721200-148735600	Weak transcription	Ovary	ovary
36	chr2:148721400-148735000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:148721400-148735000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:148721400-148735200	Weak transcription	Fetal Stomach	stomach
39	chr2:148721400-148735600	Weak transcription	Esophagus	oesophagus
40	chr2:148721400-148735600	Weak transcription	Thymus	Thymus
41	chr2:148721400-148752800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:148721400-148763600	Weak transcription	Spleen	Spleen
43	chr2:148721600-148735600	Weak transcription	Fetal Thymus	thymus
44	chr2:148722000-148731000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:148722800-148730000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:148722800-148730400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:148722800-148740400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:148722800-148740600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:148722800-148756400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:148723600-148730400	Weak transcription	Primary T cells fromperipheralblood	blood

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