Variant report

Variant	rs11113015
Chromosome Location	chr12:106894380-106894381
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	chr12:106892816..106895572-chr12:106907809..106909841,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10778483	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778484	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861600	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10861607	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10861615	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861616	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112983	0.81[EUR][1000 genomes]
rs11113012	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11113014	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11113016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11113020	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11113023	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11113025	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12231768	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13561	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532586	0.81[GIH][hapmap]
rs17038484	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243506	1.00[ASW][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap]
rs2246353	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249162	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2249773	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs2250262	0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[AMR][1000 genomes]
rs2252685	0.82[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap]
rs2288266	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288269	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374609	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34619628	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3851635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902141	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964460	0.82[MEX][hapmap]
rs741624	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11113015	POLR3B	Cis_1M	lymphoblastoid	RTeQTL
rs11113015	TCP11L2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106854600-106899800	Weak transcription	Fetal Thymus	thymus
4	chr12:106855800-106895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:106855800-106896200	Weak transcription	Thymus	Thymus
6	chr12:106856800-106899400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:106858600-106895400	Weak transcription	Fetal Heart	heart
8	chr12:106865400-106895200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:106865400-106897800	Weak transcription	Spleen	Spleen
10	chr12:106872600-106897800	Weak transcription	Psoas Muscle	Psoas
11	chr12:106884800-106899800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:106886200-106916400	Weak transcription	A549	lung
13	chr12:106887600-106895400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:106887600-106898000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine
16	chr12:106887800-106895200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:106887800-106900200	Weak transcription	Fetal Brain Male	brain
18	chr12:106888000-106899800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:106888200-106895400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:106888200-106895600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:106888200-106897800	Weak transcription	Fetal Brain Female	brain
22	chr12:106888200-106898000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:106888200-106899400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:106888200-106906800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:106888800-106900400	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:106889000-106899600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:106889200-106897200	Weak transcription	Stomach Mucosa	stomach
28	chr12:106889200-106903200	Weak transcription	HMEC	breast
29	chr12:106889200-106904600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:106889200-106905400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:106889400-106894800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:106889400-106896800	Strong transcription	Adipose Nuclei	Adipose
33	chr12:106889400-106899600	Strong transcription	Fetal Stomach	stomach
34	chr12:106889400-106904000	Strong transcription	Primary T cells from cord blood	blood
35	chr12:106889400-106904600	Strong transcription	Liver	Liver
36	chr12:106889600-106896600	Strong transcription	Ovary	ovary
37	chr12:106889800-106894800	Strong transcription	Fetal Intestine Small	intestine
38	chr12:106889800-106895400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:106889800-106896400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:106889800-106899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:106889800-106899800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:106889800-106900200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:106889800-106901600	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:106890000-106895400	Weak transcription	NHLF	lung
45	chr12:106890000-106896600	Strong transcription	Placenta	Placenta
46	chr12:106890000-106896800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr12:106890000-106904200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:106890200-106899200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:106890200-106899400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:106890400-106896200	Strong transcription	Duodenum Mucosa	Duodenum

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