Variant report

Variant	rs1471120
Chromosome Location	chr2:161028187-161028188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:161000991..161002542-chr2:161026874..161029211,2	MCF-7	breast:
2	chr2:161027893..161029945-chr2:161054838..161057768,2	MCF-7	breast:
3	chr2:161022710..161025666-chr2:161026068..161028687,2	MCF-7	breast:
4	chr2:161025898..161028586-chr2:161060919..161062605,2	MCF-7	breast:
5	chr2:161000112..161002842-chr2:161027169..161029887,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115221	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10454740	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs10497208	0.81[CEU][hapmap]
rs11887337	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11902965	0.81[CEU][hapmap]
rs12692582	0.91[EUR][1000 genomes]
rs12999707	0.81[EUR][1000 genomes]
rs13394776	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs13414434	0.91[EUR][1000 genomes]
rs13427061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1457233	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1457235	0.83[CEU][hapmap]
rs1457238	0.81[CEU][hapmap]
rs1457240	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]
rs1457241	0.89[EUR][1000 genomes]
rs1471121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844824	0.81[CEU][hapmap]
rs16844888	1.00[CHB][hapmap]
rs1840893	0.86[EUR][1000 genomes]
rs1902622	0.80[CEU][hapmap]
rs2061288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357773	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2667033	0.87[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs2715929	0.91[CEU][hapmap]
rs2925753	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925756	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925758	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925760	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[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]
rs4129787	0.80[EUR][1000 genomes]
rs4233679	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs4233680	0.80[EUR][1000 genomes]
rs4324285	0.91[CEU][hapmap]
rs4399677	0.80[EUR][1000 genomes]
rs4665155	0.81[EUR][1000 genomes]
rs6432587	0.80[EUR][1000 genomes]
rs6432590	0.80[EUR][1000 genomes]
rs6432593	0.91[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs6432602	0.80[CEU][hapmap]
rs6432603	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6720128	0.86[EUR][1000 genomes]
rs6729540	0.91[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6749513	0.81[EUR][1000 genomes]
rs748427	0.80[CEU][hapmap]
rs7558852	0.91[CEU][hapmap]
rs7569555	0.81[CEU][hapmap]
rs7579481	0.80[CEU][hapmap]
rs7583743	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs7584446	0.80[CEU][hapmap]
rs7608152	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs996112	0.96[CEU][hapmap];0.89[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1471120	PLA2R1	cis	cerebellum	SCAN
rs1471120	CYTIP	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
2	chr2:160994400-161037400	Weak transcription	Pancreas	Pancrea
3	chr2:160994600-161038000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:161002600-161028400	Weak transcription	Lung	lung
5	chr2:161005600-161037400	Weak transcription	Esophagus	oesophagus
6	chr2:161014800-161028200	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:161015000-161037400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:161016000-161030800	Strong transcription	HMEC	breast
9	chr2:161016200-161029800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:161016200-161030800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:161016400-161030200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:161020800-161028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:161021400-161029400	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr2:161022200-161030800	Strong transcription	NHEK	skin
15	chr2:161022400-161028800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:161023000-161037000	Weak transcription	Stomach Mucosa	stomach
17	chr2:161024000-161051000	Weak transcription	HSMMtube	muscle
18	chr2:161024600-161029200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:161025400-161029800	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:161025600-161051000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:161026200-161028800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:161026400-161030400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:161026400-161030800	Weak transcription	A549	lung
24	chr2:161026400-161037800	Weak transcription	Fetal Intestine Small	intestine
25	chr2:161026800-161029200	Strong transcription	HSMM	muscle
26	chr2:161026800-161037400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:161027000-161028400	Weak transcription	Fetal Kidney	kidney
28	chr2:161027200-161028400	Weak transcription	Fetal Intestine Large	intestine
29	chr2:161027200-161030200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:161027200-161051400	Weak transcription	Gastric	stomach

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