Variant report

Variant	rs17664
Chromosome Location	chr2:173369231-173369232
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	chr2:173369225..173371030-chr2:173375682..173378020,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225205	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10193201	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10460364	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11898288	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13012170	0.85[JPT][hapmap]
rs1319059	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1920979	0.95[CEU][hapmap];0.91[TSI][hapmap]
rs2357634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2357635	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2737086	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108778	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35968313	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4246629	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972834	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972835	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4972841	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs5015856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55978548	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62167825	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710725	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715425	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6723030	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6730905	0.80[EUR][1000 genomes]
rs6749369	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6759316	0.83[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs6759557	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs7560501	0.82[EUR][1000 genomes]
rs7570417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7575064	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17664	UBR3	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
3	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:173330600-173373200	Strong transcription	NHEK	skin
6	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
10	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:173331000-173373800	Strong transcription	HMEC	breast
14	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:173346000-173370200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:173346000-173370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:173346000-173370600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:173346400-173371400	Weak transcription	NHLF	lung
20	chr2:173347800-173371600	Weak transcription	Fetal Brain Male	brain
21	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
22	chr2:173349400-173370400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr2:173352000-173371400	Weak transcription	Fetal Brain Female	brain
24	chr2:173352000-173374200	Weak transcription	Fetal Lung	lung
25	chr2:173352400-173371400	Weak transcription	Psoas Muscle	Psoas
26	chr2:173354000-173370400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:173356600-173371400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:173356600-173375400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:173356800-173374600	Weak transcription	Fetal Kidney	kidney
31	chr2:173356800-173376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:173357000-173371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:173357000-173371200	Weak transcription	Ovary	ovary
35	chr2:173357000-173373000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:173357000-173376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:173357000-173376000	Weak transcription	Aorta	Aorta
38	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
39	chr2:173357600-173371400	Weak transcription	NH-A	brain
40	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:173359200-173371400	Weak transcription	Lung	lung
43	chr2:173359200-173372400	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:173360400-173371400	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:173360800-173371800	Weak transcription	Thymus	Thymus
46	chr2:173361000-173371000	Weak transcription	Fetal Stomach	stomach
47	chr2:173361000-173375600	Weak transcription	Spleen	Spleen
48	chr2:173361200-173371000	Weak transcription	Small Intestine	intestine
49	chr2:173361200-173373600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr2:173361200-173375200	Weak transcription	GM12878-XiMat	blood

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