Variant report

Variant	rs4771270
Chromosome Location	chr13:97973721-97973722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:97965578..97967937-chr13:97972891..97974672,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1316549	0.84[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]
rs1463790	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1553012	0.83[CHB][hapmap]
rs1553013	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973419	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2011452	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291785	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782983	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.82[AMR][1000 genomes]
rs61974439	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6491350	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap]
rs7320865	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7338689	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7995199	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949741	0.89[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9513235	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9513237	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9516902	0.89[ASW][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs9516904	0.84[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]
rs9516907	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516914	0.82[AMR][1000 genomes]
rs9556701	0.83[CHB][hapmap]
rs9556702	0.87[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556706	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4771270	GPR18	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97925800-97987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr13:97942800-97995200	Weak transcription	Thymus	Thymus
3	chr13:97954400-97986200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr13:97955000-97987000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:97955200-97986800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:97959400-97988800	Weak transcription	Fetal Intestine Large	intestine
7	chr13:97961000-97973800	Weak transcription	NHEK	skin
8	chr13:97961400-97975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:97961400-97987200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:97961600-97975400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:97961800-97975200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:97961800-97977600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:97961800-97978000	Weak transcription	HMEC	breast
14	chr13:97962000-97979200	Weak transcription	HUVEC	blood vessel
15	chr13:97962000-97991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:97962400-97978200	Weak transcription	K562	blood
17	chr13:97963000-97984400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:97963600-97977000	Weak transcription	Hela-S3	cervix
19	chr13:97965200-97985800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:97965600-97988800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr13:97965800-97987200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr13:97967000-97980400	Weak transcription	Fetal Thymus	thymus
23	chr13:97967400-97991400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr13:97969200-97979200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:97969400-97981600	Weak transcription	Spleen	Spleen
26	chr13:97969400-97981800	Weak transcription	Esophagus	oesophagus
27	chr13:97969600-97982000	Weak transcription	Primary B cells from cord blood	blood
28	chr13:97969600-97987200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr13:97969800-97986600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr13:97971400-97975000	Weak transcription	NH-A	brain
31	chr13:97971400-97979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:97971400-97981800	Weak transcription	Gastric	stomach
33	chr13:97971600-97974000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:97971600-97979800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr13:97971600-97981600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:97971600-97991400	Weak transcription	Stomach Mucosa	stomach
37	chr13:97971800-97973800	Weak transcription	Fetal Stomach	stomach
38	chr13:97971800-97974000	Weak transcription	Adipose Nuclei	Adipose
39	chr13:97971800-97974000	Weak transcription	Lung	lung
40	chr13:97971800-97974200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:97971800-97975200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr13:97971800-97979800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:97971800-97980200	Weak transcription	Placenta	Placenta
44	chr13:97971800-97980600	Weak transcription	Pancreas	Pancrea
45	chr13:97971800-97981600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr13:97971800-97986400	Weak transcription	Primary T cells from cord blood	blood
47	chr13:97971800-97986400	Weak transcription	Aorta	Aorta
48	chr13:97971800-97986400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr13:97971800-97987200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:97971800-97987600	Weak transcription	Fetal Intestine Small	intestine

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