Variant report

Variant	rs17310361
Chromosome Location	chr11:73233724-73233725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73231178..73234417-chr11:73236795..73240578,4	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1002127	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10047427	1.00[MEX][hapmap]
rs10501411	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10751226	1.00[CHB][hapmap]
rs11235744	1.00[MEX][hapmap]
rs11235756	1.00[MEX][hapmap]
rs11235770	1.00[CEU][hapmap]
rs11235782	1.00[MEX][hapmap]
rs11235809	1.00[CEU][hapmap]
rs11235817	1.00[MEX][hapmap]
rs11820577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11821094	0.89[CEU][hapmap]
rs11822984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11823913	1.00[CEU][hapmap]
rs11828904	1.00[CEU][hapmap]
rs12274057	0.89[AFR][1000 genomes]
rs12276892	1.00[CEU][hapmap]
rs12277924	0.82[EUR][1000 genomes]
rs12281470	1.00[MEX][hapmap]
rs12282576	1.00[MEX][hapmap]
rs12285885	1.00[CEU][hapmap]
rs12288753	1.00[CEU][hapmap]
rs12290623	1.00[CEU][hapmap]
rs12290785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17244596	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17244602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17244616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17310374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17851510	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1938777	1.00[CEU][hapmap]
rs2008722	1.00[MEX][hapmap]
rs2027760	0.89[CEU][hapmap]
rs2027761	0.89[CEU][hapmap]
rs2027763	0.89[CEU][hapmap]
rs2298469	1.00[CEU][hapmap]
rs56742470	0.88[EUR][1000 genomes]
rs56857598	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56884659	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57491850	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57673166	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564192	0.97[EUR][1000 genomes]
rs594814	1.00[MEX][hapmap]
rs610280	1.00[MEX][hapmap]
rs6592526	0.88[EUR][1000 genomes]
rs7101561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7105681	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7110369	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs7114009	1.00[CEU][hapmap]
rs7114376	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7115055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7118982	1.00[CEU][hapmap]
rs7122825	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7123985	1.00[CEU][hapmap]
rs7125598	1.00[CEU][hapmap]
rs7125978	0.89[CEU][hapmap]
rs7129546	0.88[EUR][1000 genomes]
rs7129990	0.89[CEU][hapmap]
rs724111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73544767	0.88[EUR][1000 genomes]
rs73544783	1.00[EUR][1000 genomes]
rs73546720	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73546735	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73548680	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73548688	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73548693	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73550316	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs7930152	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7930454	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs7930880	0.89[CEU][hapmap]
rs7931767	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7933355	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7934218	1.00[CEU][hapmap]
rs7935948	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7941359	1.00[CEU][hapmap]
rs7944346	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7945825	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7950375	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7951072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv508641	chr11:73149281-73235528	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1048171	chr11:73210060-73271831	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17310361	ARHGEF17	cis	Whole Blood	GTEx
rs17310361	P2RY2	cis	cerebellum	SCAN
rs17310361	CCND1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73202400-73240000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:73205000-73239600	Weak transcription	Primary B cells from cord blood	blood
3	chr11:73205600-73236400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:73205800-73241400	Weak transcription	Pancreas	Pancrea
5	chr11:73219200-73241400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:73221200-73238000	Weak transcription	Psoas Muscle	Psoas
7	chr11:73221400-73238200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:73221800-73239600	Weak transcription	Liver	Liver
9	chr11:73226400-73239600	Weak transcription	Fetal Stomach	stomach
10	chr11:73230000-73233800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr11:73230000-73234600	Enhancers	Dnd41	blood
12	chr11:73230800-73239600	Weak transcription	NHDF-Ad	bronchial
13	chr11:73231400-73233800	Enhancers	Primary T cells from cord blood	blood
14	chr11:73232600-73239800	Weak transcription	Thymus	Thymus
15	chr11:73232600-73249400	Weak transcription	Brain Germinal Matrix	brain
16	chr11:73232800-73235600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:73233000-73234000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:73233000-73234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:73233000-73234600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:73233000-73234600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:73233000-73236400	Weak transcription	Brain Anterior Caudate	brain
22	chr11:73233000-73237600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:73233000-73237600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:73233000-73238000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:73233000-73238200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:73233000-73239600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:73233000-73239600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:73233000-73239600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:73233000-73240000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr11:73233000-73241400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:73233200-73237400	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:73233200-73237400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:73233200-73237600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:73233200-73238000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:73233200-73238000	Weak transcription	Brain Angular Gyrus	brain
36	chr11:73233200-73238000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:73233200-73238000	Weak transcription	NH-A	brain
38	chr11:73233200-73238200	Weak transcription	Osteobl	bone
39	chr11:73233400-73234000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:73233400-73237400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:73233400-73237400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:73233400-73238200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:73233400-73239200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:73233400-73239200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:73233600-73234000	Weak transcription	Brain Substantia Nigra	brain

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