Variant report

Variant	rs13006483
Chromosome Location	chr2:187522750-187522751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187512598..187514600-chr2:187521412..187523293,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10171481	0.85[CHB][hapmap]
rs10804007	0.85[CHB][hapmap]
rs11678190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs11685758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12151442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12615659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12998294	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13001028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13006571	0.85[CHB][hapmap]
rs13016261	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13026081	0.87[CEU][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs13027560	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13028817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13030356	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs13033579	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1448424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs17334303	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17334422	1.00[CHB][hapmap]
rs17406339	1.00[CHB][hapmap]
rs17750683	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs1839121	0.93[EUR][1000 genomes]
rs1839123	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1839124	0.95[EUR][1000 genomes]
rs1992898	0.85[CHB][hapmap]
rs2084448	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2165656	0.85[CHB][hapmap]
rs2197138	0.85[CHB][hapmap]
rs2197787	0.84[CHB][hapmap]
rs2370693	0.85[CHB][hapmap]
rs2595375	0.85[CHB][hapmap];0.85[TSI][hapmap]
rs2887827	0.85[CHB][hapmap]
rs34483988	0.86[EUR][1000 genomes]
rs34521209	0.80[ASN][1000 genomes]
rs34980163	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35251833	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35986780	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3768778	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs3768780	0.85[CHB][hapmap]
rs3816386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3911084	0.85[CHB][hapmap]
rs4233788	0.85[CHB][hapmap]
rs6717512	1.00[CHB][hapmap]
rs6741369	0.85[CHB][hapmap]
rs6748509	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6753438	0.85[EUR][1000 genomes]
rs7419327	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7575516	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7589470	1.00[CHB][hapmap]
rs7596996	0.85[CHB][hapmap]
rs9333287	0.85[CHB][hapmap]
rs9333288	0.85[CHB][hapmap]
rs9333289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9333290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs998972	1.00[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13006483	FAM171B	cis	parietal	SCAN
rs13006483	FAM171B	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
4	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:187464800-187536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:187465800-187529200	Weak transcription	Dnd41	blood
7	chr2:187466800-187533200	Weak transcription	Colonic Mucosa	Colon
8	chr2:187467200-187528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:187476800-187536200	Weak transcription	Fetal Brain Male	brain
10	chr2:187482200-187533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:187482800-187527800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:187482800-187533200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:187482800-187533600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:187482800-187533800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:187482800-187533800	Weak transcription	Psoas Muscle	Psoas
16	chr2:187486600-187531400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:187489400-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:187493800-187529200	Weak transcription	Brain Substantia Nigra	brain
19	chr2:187494200-187529200	Weak transcription	Brain Germinal Matrix	brain
20	chr2:187494200-187535800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:187494800-187531800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:187495000-187534400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:187501000-187548400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:187502800-187533000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:187503400-187545000	Weak transcription	Hela-S3	cervix
26	chr2:187504200-187529400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:187505400-187533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:187505600-187527600	Weak transcription	Fetal Heart	heart
29	chr2:187505800-187528800	Weak transcription	Stomach Mucosa	stomach
30	chr2:187506600-187529600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:187506600-187533400	Weak transcription	NHLF	lung
32	chr2:187506600-187537000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:187507200-187529200	Weak transcription	Fetal Brain Female	brain
34	chr2:187507400-187529000	Weak transcription	Primary T cells from cord blood	blood
35	chr2:187507800-187529200	Weak transcription	GM12878-XiMat	blood
36	chr2:187507800-187546600	Weak transcription	Small Intestine	intestine
37	chr2:187508000-187529200	Weak transcription	NHEK	skin
38	chr2:187510200-187529200	Weak transcription	Pancreas	Pancrea
39	chr2:187510800-187535000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:187511200-187536200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:187511400-187546600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:187511600-187545000	Strong transcription	Osteobl	bone
43	chr2:187512400-187529200	Weak transcription	Ovary	ovary
44	chr2:187512600-187529200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:187513000-187531800	Weak transcription	Brain Angular Gyrus	brain
46	chr2:187513400-187525600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:187513800-187523800	Strong transcription	HSMM	muscle
48	chr2:187513800-187546800	Strong transcription	NH-A	brain
49	chr2:187514600-187546200	Strong transcription	Placenta	Placenta
50	chr2:187515200-187536200	Weak transcription	Primary B cells from cord blood	blood

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