Variant report

Variant	rs12105745
Chromosome Location	chr2:148673662-148673663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1014064	0.96[YRI][hapmap]
rs1015096	0.96[YRI][hapmap]
rs10180655	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10439198	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10460259	0.96[YRI][hapmap]
rs10803523	0.96[YRI][hapmap]
rs1128919	0.96[YRI][hapmap]
rs11686483	0.96[ASN][1000 genomes]
rs11886876	0.96[YRI][hapmap]
rs11888152	0.95[YRI][hapmap]
rs11900506	0.96[YRI][hapmap]
rs11901963	0.96[YRI][hapmap]
rs12053401	0.91[YRI][hapmap]
rs1227304	0.89[ASN][1000 genomes]
rs1234416	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs12463798	0.96[YRI][hapmap]
rs12622150	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12989087	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12989250	0.96[YRI][hapmap]
rs12990959	0.92[YRI][hapmap]
rs12992412	0.95[YRI][hapmap]
rs13016400	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs13016893	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs13019809	0.96[YRI][hapmap]
rs13021605	0.95[YRI][hapmap]
rs13021972	0.82[AFR][1000 genomes]
rs13022962	0.87[YRI][hapmap]
rs13026650	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs13027706	0.95[YRI][hapmap]
rs13028348	0.96[YRI][hapmap]
rs13033696	0.96[YRI][hapmap]
rs13430086	0.92[ASN][1000 genomes]
rs1424954	0.96[YRI][hapmap]
rs1469210	0.96[YRI][hapmap]
rs1531032	0.92[YRI][hapmap]
rs1598207	0.96[YRI][hapmap]
rs1863152	0.96[YRI][hapmap]
rs1863153	0.88[YRI][hapmap]
rs1895694	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1975748	0.96[YRI][hapmap]
rs1991169	0.96[YRI][hapmap]
rs2113792	0.81[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs2113793	0.96[YRI][hapmap]
rs2113794	0.94[ASN][1000 genomes]
rs2161983	0.90[YRI][hapmap]
rs2161984	0.96[YRI][hapmap]
rs2194695	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2303392	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2307394	0.96[YRI][hapmap]
rs2603597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2603600	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2627019	0.87[ASN][1000 genomes]
rs2627025	0.86[ASN][1000 genomes]
rs3768684	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3768686	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3768688	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768689	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs3820716	0.96[CEU][hapmap];0.95[JPT][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4419186	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55816333	0.91[ASN][1000 genomes]
rs56073268	0.91[ASN][1000 genomes]
rs6709182	0.81[CEU][hapmap]
rs6711673	0.96[YRI][hapmap]
rs6713811	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6731371	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6734998	0.96[YRI][hapmap]
rs755365	0.82[EUR][1000 genomes]
rs7566230	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7582403	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7593570	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897172	0.96[YRI][hapmap]
rs9287411	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs929939	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12105745	ORC4L	Cis_1M	lymphoblastoid	RTeQTL
rs12105745	MMADHC	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148642800-148674600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:148646200-148684400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:148646600-148691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:148647200-148719600	Weak transcription	Pancreas	Pancrea
6	chr2:148649600-148674800	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:148650200-148719600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:148651200-148691600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:148652800-148690000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:148652800-148693600	Weak transcription	Lung	lung
11	chr2:148653200-148692000	Weak transcription	Ovary	ovary
12	chr2:148653200-148719600	Weak transcription	Esophagus	oesophagus
13	chr2:148654000-148690000	Weak transcription	Primary T cells from cord blood	blood
14	chr2:148655200-148674800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:148656200-148676800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:148657800-148674400	Weak transcription	Fetal Kidney	kidney
17	chr2:148657800-148674400	Weak transcription	Left Ventricle	heart
18	chr2:148657800-148683000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:148658600-148674400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
21	chr2:148659600-148719800	Weak transcription	Gastric	stomach
22	chr2:148661600-148718200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:148662000-148683800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:148663000-148692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:148664600-148721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:148664800-148693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:148668600-148674800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:148668600-148682400	Weak transcription	Psoas Muscle	Psoas
29	chr2:148668600-148683600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:148668600-148691800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:148668800-148683400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:148669200-148678000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:148670600-148690200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:148670800-148674800	Enhancers	Rectal Smooth Muscle	rectum
35	chr2:148671200-148690200	Weak transcription	Placenta	Placenta
36	chr2:148671600-148690200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:148671800-148674200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:148671800-148674400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:148671800-148676400	Weak transcription	HSMMtube	muscle
40	chr2:148671800-148677800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:148671800-148679000	Weak transcription	NHDF-Ad	bronchial
42	chr2:148671800-148680200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:148671800-148683200	Weak transcription	Fetal Brain Male	brain
44	chr2:148671800-148683600	Weak transcription	Osteobl	bone
45	chr2:148671800-148687400	Weak transcription	NH-A	brain
46	chr2:148671800-148690200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:148671800-148691800	Weak transcription	NHLF	lung
48	chr2:148671800-148692000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:148671800-148698800	Weak transcription	NHEK	skin
50	chr2:148671800-148719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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