Variant report

Variant	rs9287411
Chromosome Location	chr2:148623304-148623305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:148621910..148624098-chr2:148629149..148631305,2	MCF-7	breast:
2	chr2:148618900..148620557-chr2:148620956..148623772,2	MCF-7	breast:
3	chr2:148379769..148381689-chr2:148622128..148624612,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10180655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11686483	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12105745	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1227304	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234416	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12622150	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12989087	0.97[ASN][1000 genomes]
rs13016400	0.81[CEU][hapmap]
rs13016893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13430086	0.89[CEU][hapmap];0.93[ASN][1000 genomes]
rs1895694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042555	0.83[EUR][1000 genomes]
rs2113792	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113794	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288190	0.93[YRI][hapmap]
rs2603597	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2603600	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2627019	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627025	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3768684	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3768686	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3768688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820716	0.89[CEU][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4419186	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs55816333	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56073268	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6709182	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6713811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731371	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7566230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7582403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593570	0.88[ASN][1000 genomes]
rs998884	0.82[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9287411	ORC4L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148606000-148627600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:148613000-148627400	Weak transcription	Pancreas	Pancrea
3	chr2:148613000-148640800	Weak transcription	Lung	lung
4	chr2:148613200-148625600	Weak transcription	Right Atrium	heart
5	chr2:148613200-148631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:148615800-148626200	Weak transcription	Ovary	ovary
7	chr2:148616800-148636200	Weak transcription	Small Intestine	intestine
8	chr2:148617800-148624400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:148618000-148625400	Weak transcription	Right Ventricle	heart
10	chr2:148618000-148625600	Weak transcription	HSMMtube	muscle
11	chr2:148618000-148627400	Weak transcription	Fetal Brain Male	brain
12	chr2:148618000-148627400	Weak transcription	Gastric	stomach
13	chr2:148618400-148626800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:148618400-148627400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:148618600-148626800	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:148618600-148627000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:148620000-148634000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:148620400-148623400	Weak transcription	Psoas Muscle	Psoas
19	chr2:148620600-148634200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:148620800-148627000	Weak transcription	Fetal Intestine Small	intestine
21	chr2:148620800-148640000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:148621000-148624200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:148621000-148624400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:148621000-148624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:148621000-148624400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:148621000-148624800	Weak transcription	Primary T cells from cord blood	blood
27	chr2:148621000-148625400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:148621000-148627000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:148621000-148627400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:148621200-148624000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:148621200-148624600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:148621200-148626800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:148621200-148633600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:148621400-148624400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:148621400-148624600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:148621400-148633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:148621400-148637000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:148621600-148631400	Weak transcription	Stomach Mucosa	stomach
39	chr2:148621600-148641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:148621800-148624600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:148621800-148628000	Weak transcription	HMEC	breast
42	chr2:148622000-148626200	Weak transcription	HUVEC	blood vessel
43	chr2:148622600-148623600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:148622600-148623800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr2:148622800-148623800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:148623000-148623400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:148623000-148623600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:148623000-148623600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:148623000-148624000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr2:148623000-148624400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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