Variant report

Variant	rs12772737
Chromosome Location	chr10:116741501-116741502
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116734818..116737513-chr10:116740129..116742144,2	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10160015	0.90[ASN][1000 genomes]
rs10444099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1045657	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.81[ASN][1000 genomes]
rs10885632	0.81[ASN][1000 genomes]
rs10885633	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10885638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs10885639	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11196983	0.81[ASN][1000 genomes]
rs11196984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11196989	0.81[ASN][1000 genomes]
rs11196991	0.95[ASN][1000 genomes]
rs11196996	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs11196999	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs11197000	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197005	0.95[ASN][1000 genomes]
rs11197006	0.87[ASN][1000 genomes]
rs11197007	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197011	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs11197012	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197023	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12246008	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12265048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12269261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12761122	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774597	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17722042	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.95[ASN][1000 genomes]
rs2105001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2420070	0.81[ASN][1000 genomes]
rs34170154	1.00[ASN][1000 genomes]
rs34318200	0.81[EUR][1000 genomes]
rs34434610	1.00[ASN][1000 genomes]
rs34453431	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34461950	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35501899	1.00[ASN][1000 genomes]
rs35811923	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931556	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs61869271	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869272	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869274	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869275	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585302	0.81[ASN][1000 genomes]
rs6585306	0.95[ASN][1000 genomes]
rs6585308	0.84[CEU][hapmap]
rs6585309	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585310	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585311	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585313	1.00[ASN][1000 genomes]
rs7071789	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7071812	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085964	0.90[ASN][1000 genomes]
rs7086663	0.81[CEU][hapmap]
rs7093282	0.87[ASN][1000 genomes]
rs7093330	1.00[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099590	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099779	0.95[ASN][1000 genomes]
rs7100026	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100159	0.95[ASN][1000 genomes]
rs7100894	0.81[ASN][1000 genomes]
rs72836518	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7904605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7908069	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7908464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs968848	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968849	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12772737	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs12772737	ATRNL1	cis	Muscle Skeletal	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
2	chr10:116703600-116747800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:116707000-116744200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:116707000-116745600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr10:116708800-116742000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:116716400-116743200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:116718000-116747600	Weak transcription	Osteobl	bone
8	chr10:116722800-116744400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr10:116722800-116748000	Weak transcription	Aorta	Aorta
10	chr10:116723000-116741800	Weak transcription	NHEK	skin
11	chr10:116723000-116742000	Weak transcription	Fetal Intestine Large	intestine
12	chr10:116723000-116742200	Weak transcription	Lung	lung
13	chr10:116723000-116742400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr10:116723000-116743400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:116723000-116744000	Weak transcription	Gastric	stomach
16	chr10:116723000-116760800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr10:116723200-116742000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr10:116723200-116742200	Weak transcription	HMEC	breast
19	chr10:116723200-116743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:116723600-116744200	Weak transcription	NH-A	brain
21	chr10:116724000-116742000	Weak transcription	A549	lung
22	chr10:116724000-116742600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:116724600-116742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr10:116727000-116743400	Weak transcription	HUVEC	blood vessel
25	chr10:116728400-116742000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:116728400-116743600	Weak transcription	HSMM	muscle
27	chr10:116730400-116743800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr10:116730600-116742000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:116730600-116742200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr10:116730600-116743400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:116730800-116744000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr10:116731000-116742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:116731000-116761200	Weak transcription	Pancreas	Pancrea
34	chr10:116731200-116743200	Weak transcription	HepG2	liver
35	chr10:116732800-116744600	Weak transcription	Stomach Mucosa	stomach
36	chr10:116734400-116752000	Weak transcription	Brain Angular Gyrus	brain
37	chr10:116734600-116744200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr10:116735000-116742000	Weak transcription	HSMMtube	muscle
39	chr10:116735200-116741800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr10:116735200-116742000	Weak transcription	Fetal Muscle Leg	muscle
41	chr10:116735200-116742000	Weak transcription	Psoas Muscle	Psoas
42	chr10:116735200-116742400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:116735200-116742400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr10:116735200-116742400	Weak transcription	Liver	Liver
45	chr10:116735200-116743400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr10:116735200-116751800	Weak transcription	Ovary	ovary
47	chr10:116735400-116742000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:116735400-116742000	Weak transcription	Brain Substantia Nigra	brain
49	chr10:116735400-116742200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr10:116735400-116742200	Weak transcription	Adipose Nuclei	Adipose

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