Variant report

Variant	rs2288190
Chromosome Location	chr2:148657589-148657590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1014064	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1015096	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1030317	0.85[ASN][1000 genomes]
rs10460259	0.84[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10497024	0.84[CEU][hapmap]
rs10803523	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs1128919	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs11886876	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs11888152	0.84[CEU][hapmap];0.81[CHD][hapmap]
rs11889608	0.90[ASN][1000 genomes]
rs11901963	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11904758	0.92[ASN][1000 genomes]
rs12053113	0.87[ASN][1000 genomes]
rs12053401	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs12104822	0.85[ASN][1000 genomes]
rs12463798	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12464617	0.90[ASN][1000 genomes]
rs12469504	0.83[ASN][1000 genomes]
rs12622150	0.86[YRI][hapmap]
rs12987286	0.84[CEU][hapmap]
rs12989250	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs12990262	0.83[ASN][1000 genomes]
rs12992412	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12998729	0.84[CEU][hapmap]
rs13000597	0.97[ASN][1000 genomes]
rs13004451	0.95[ASN][1000 genomes]
rs13008497	0.84[CEU][hapmap]
rs13012311	0.85[ASN][1000 genomes]
rs13013867	0.90[ASN][1000 genomes]
rs13019809	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs13021605	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs13022962	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs13025219	0.94[ASN][1000 genomes]
rs13025589	0.90[ASN][1000 genomes]
rs13026650	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs13027706	0.83[CEU][hapmap]
rs13028348	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs13028411	0.95[ASN][1000 genomes]
rs13033589	0.85[ASN][1000 genomes]
rs13033696	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs13034793	0.85[ASN][1000 genomes]
rs1345994	0.81[ASN][1000 genomes]
rs1364658	0.84[CEU][hapmap]
rs1424944	0.82[CEU][hapmap];0.90[ASN][1000 genomes]
rs1424954	0.84[CEU][hapmap];0.89[ASN][1000 genomes]
rs1469210	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1531032	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1598207	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1895693	0.97[ASN][1000 genomes]
rs1975748	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2059422	0.87[ASN][1000 genomes]
rs2113793	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2161983	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2161984	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2303392	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2307394	0.84[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2382201	0.84[CEU][hapmap]
rs3764955	0.84[CEU][hapmap]
rs3768687	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3768689	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4972317	0.84[ASN][1000 genomes]
rs4972318	0.83[ASN][1000 genomes]
rs4972322	0.81[JPT][hapmap]
rs4972357	0.86[ASN][1000 genomes]
rs6709182	0.93[YRI][hapmap]
rs6711673	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6760703	0.86[ASN][1000 genomes]
rs723681	0.84[CEU][hapmap]
rs7559714	0.92[ASN][1000 genomes]
rs7566230	0.93[YRI][hapmap]
rs7582403	0.93[YRI][hapmap]
rs7598361	0.84[CEU][hapmap]
rs897172	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs9287411	0.93[YRI][hapmap]
rs929939	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2288190	ORC4L	cis	parietal	SCAN
rs2288190	ACVR2A	cis	Liver	GTEx
rs2288190	ACVR2A	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148634600-148668200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
3	chr2:148642600-148668200	Weak transcription	Psoas Muscle	Psoas
4	chr2:148642800-148668200	Weak transcription	Fetal Lung	lung
5	chr2:148642800-148670800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:148642800-148674600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:148643200-148660000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:148643200-148663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:148645600-148671000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:148645800-148671400	Weak transcription	Fetal Heart	heart
11	chr2:148646000-148660600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:148646200-148684400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:148646600-148663800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:148646600-148668400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:148646600-148671200	Weak transcription	HMEC	breast
16	chr2:148646600-148691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:148646800-148657600	Weak transcription	Adipose Nuclei	Adipose
18	chr2:148647200-148719600	Weak transcription	Pancreas	Pancrea
19	chr2:148649600-148674800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:148650200-148719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:148650800-148663400	Weak transcription	HUVEC	blood vessel
22	chr2:148651200-148691600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:148651800-148658800	Weak transcription	Brain Germinal Matrix	brain
24	chr2:148652800-148690000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:148652800-148693600	Weak transcription	Lung	lung
26	chr2:148653200-148692000	Weak transcription	Ovary	ovary
27	chr2:148653200-148719600	Weak transcription	Esophagus	oesophagus
28	chr2:148653600-148671000	Weak transcription	Osteobl	bone
29	chr2:148653600-148671400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:148653600-148673400	Weak transcription	HepG2	liver
31	chr2:148653800-148671600	Weak transcription	Fetal Stomach	stomach
32	chr2:148653800-148672800	Weak transcription	Liver	Liver
33	chr2:148654000-148690000	Weak transcription	Primary T cells from cord blood	blood
34	chr2:148654400-148664400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:148654600-148657600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:148654800-148658000	Strong transcription	Fetal Intestine Large	intestine
37	chr2:148655200-148674800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:148655400-148671600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:148655800-148671000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:148655800-148671200	Weak transcription	Fetal Brain Male	brain
41	chr2:148656000-148668800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:148656200-148676800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:148656400-148660200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:148656400-148660400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:148656800-148659200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:148656800-148661000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:148657000-148657800	Strong transcription	Fetal Kidney	kidney
48	chr2:148657000-148658200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:148657000-148661800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:148657200-148657800	Strong transcription	Left Ventricle	heart

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