Variant report

Variant	rs1457240
Chromosome Location	chr2:161014184-161014185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:160997062..160999873-chr2:161011563..161014295,2	MCF-7	breast:
2	chr2:161009313..161012082-chr2:161014084..161016057,3	MCF-7	breast:
3	chr2:161011380..161016239-chr2:161062030..161067547,8	MCF-7	breast:
4	chr2:161011705..161015715-chr2:161083220..161088389,8	MCF-7	breast:
5	chr2:161011213..161014505-chr2:161097199..161099716,3	MCF-7	breast:
6	chr2:161012600..161015178-chr2:161083788..161087804,4	MCF-7	breast:
7	chr2:161011918..161014903-chr2:161016994..161018899,2	K562	blood:
8	chr2:161011444..161016530-chr2:161074862..161081219,9	MCF-7	breast:
9	chr2:161011891..161014884-chr2:161060421..161064713,4	MCF-7	breast:
10	chr2:161012780..161016073-chr2:161064751..161067692,4	MCF-7	breast:
11	chr2:161012044..161015956-chr2:161077276..161081023,8	MCF-7	breast:
12	chr2:161011673..161014390-chr2:161015333..161017860,2	MCF-7	breast:

No data

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10454740	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10497208	0.81[CEU][hapmap]
rs10803761	0.82[EUR][1000 genomes]
rs11887337	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs11902965	0.81[CEU][hapmap]
rs12692582	0.95[EUR][1000 genomes]
rs12999707	0.85[EUR][1000 genomes]
rs13031600	0.82[EUR][1000 genomes]
rs13394776	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs13414434	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13427061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1457233	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1457235	0.83[CEU][hapmap]
rs1457238	0.81[CEU][hapmap]
rs1457241	0.93[EUR][1000 genomes]
rs1471120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844824	0.81[CEU][hapmap]
rs16844888	1.00[CHB][hapmap]
rs1840893	0.89[EUR][1000 genomes]
rs1902622	0.80[CEU][hapmap]
rs2061288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357773	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs2667033	1.00[ASW][hapmap];0.87[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs2715929	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2715933	1.00[YRI][hapmap]
rs2925753	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925756	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925758	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925760	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs4129787	0.83[EUR][1000 genomes]
rs4233679	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4233680	0.83[EUR][1000 genomes]
rs4324285	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4368286	0.82[EUR][1000 genomes]
rs4399677	0.83[EUR][1000 genomes]
rs4665155	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6432582	0.81[EUR][1000 genomes]
rs6432587	0.83[EUR][1000 genomes]
rs6432590	0.83[EUR][1000 genomes]
rs6432593	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6432602	0.80[CEU][hapmap]
rs6432603	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6720128	0.90[EUR][1000 genomes]
rs6729540	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs6749513	0.85[EUR][1000 genomes]
rs6761082	0.82[EUR][1000 genomes]
rs748427	0.80[CEU][hapmap]
rs7558852	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7569555	0.81[CEU][hapmap]
rs7579481	0.80[CEU][hapmap]
rs7583743	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs7584446	0.80[CEU][hapmap]
rs7601113	1.00[YRI][hapmap]
rs7608152	0.88[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs996112	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv528083	chr2:160998792-161015066	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1457240	PLA2R1	cis	cerebellum	SCAN
rs1457240	BCR	trans	lymphoblastoid	seeQTL
rs1457240	CYTIP	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
2	chr2:160994400-161014800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:160994400-161037400	Weak transcription	Pancreas	Pancrea
4	chr2:160994600-161038000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:160997200-161014600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:160997200-161021800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr2:160999400-161022600	Weak transcription	Stomach Mucosa	stomach
8	chr2:161002600-161028400	Weak transcription	Lung	lung
9	chr2:161002800-161014600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:161003000-161021400	Weak transcription	Fetal Intestine Small	intestine
11	chr2:161005600-161022200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:161005600-161026000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:161005600-161037400	Weak transcription	Esophagus	oesophagus
14	chr2:161005800-161021800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:161012400-161015000	Enhancers	HUVEC	blood vessel
16	chr2:161012600-161015200	Enhancers	HSMM	muscle
17	chr2:161012800-161014200	Enhancers	Osteobl	bone
18	chr2:161012800-161014400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:161012800-161015000	Enhancers	A549	lung
20	chr2:161012800-161015200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:161012800-161015200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:161013000-161014200	Weak transcription	Placenta	Placenta
23	chr2:161013000-161015000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:161013200-161014200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:161013200-161014600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:161013400-161014200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:161013600-161014400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:161013600-161014400	Weak transcription	Left Ventricle	heart
29	chr2:161013600-161014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:161013600-161014600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:161013600-161014600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:161013600-161014600	Weak transcription	Ovary	ovary
33	chr2:161013600-161014800	Enhancers	NHEK	skin
34	chr2:161013600-161015200	Enhancers	HMEC	breast
35	chr2:161013600-161015400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:161013800-161014200	Weak transcription	Hela-S3	cervix
37	chr2:161013800-161015400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:161013800-161015400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr2:161013800-161016400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:161014000-161014400	Weak transcription	Right Atrium	heart
41	chr2:161014000-161014400	Weak transcription	NH-A	brain
42	chr2:161014000-161014600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:161014000-161015000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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