Variant report

Variant	rs12465802
Chromosome Location	chr2:136381348-136381349
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	chr2:136376000..136378009-chr2:136381183..136383138,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1446585	1.00[ASW][hapmap];0.94[AFR][1000 genomes]
rs182549	0.83[AFR][1000 genomes]
rs3940549	1.00[AFR][1000 genomes]
rs4988235	0.83[AFR][1000 genomes]
rs56369224	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62168795	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6709525	0.94[AFR][1000 genomes]
rs6735329	0.89[AFR][1000 genomes]
rs6759321	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34026	chr2:136049982-136537952	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	309 gene(s)	inside rSNPs	diseases
2	nsv1014238	chr2:136258388-136391449	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2830371	chr2:136261798-136394456	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1000750	chr2:136276554-136445315	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	301 gene(s)	inside rSNPs	diseases
5	esv1831223	chr2:136337874-136467164	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	290 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12465802	R3HDM1	cis	cerebellum	SCAN
rs12465802	MCM6	cis	cerebellum	SCAN
rs12465802	MCM6	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:136329800-136409200	Weak transcription	Aorta	Aorta
2	chr2:136346000-136395000	Weak transcription	Fetal Brain Male	brain
3	chr2:136347000-136409400	Weak transcription	Right Ventricle	heart
4	chr2:136348600-136393200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:136349800-136392600	Weak transcription	HMEC	breast
6	chr2:136349800-136409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:136350000-136396200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:136352200-136393200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:136352200-136418800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:136353200-136415000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:136356000-136394600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:136356000-136409200	Weak transcription	NHLF	lung
13	chr2:136358000-136399200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:136358200-136402800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:136358800-136393200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:136359600-136392800	Weak transcription	Placenta	Placenta
17	chr2:136359600-136394800	Weak transcription	Pancreas	Pancrea
18	chr2:136359800-136394600	Weak transcription	Fetal Kidney	kidney
19	chr2:136360400-136398800	Weak transcription	Small Intestine	intestine
20	chr2:136360600-136394600	Weak transcription	HUVEC	blood vessel
21	chr2:136360600-136401800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:136361200-136394600	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:136361400-136403000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:136361600-136409200	Weak transcription	Ovary	ovary
25	chr2:136361800-136393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:136361800-136394600	Weak transcription	Lung	lung
27	chr2:136362200-136394600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:136362200-136403000	Weak transcription	Hela-S3	cervix
29	chr2:136362400-136415000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:136363800-136383600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:136363800-136391800	Weak transcription	Fetal Intestine Small	intestine
32	chr2:136363800-136394400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:136363800-136394600	Weak transcription	Fetal Lung	lung
34	chr2:136364000-136382000	Weak transcription	Thymus	Thymus
35	chr2:136364000-136383600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:136364000-136392800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:136364000-136392800	Weak transcription	A549	lung
38	chr2:136364000-136393400	Weak transcription	HSMM	muscle
39	chr2:136364000-136394400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:136364000-136394400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:136364000-136394600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:136364000-136394600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:136364000-136394600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:136364000-136396400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:136364000-136402800	Weak transcription	Osteobl	bone
46	chr2:136364000-136403200	Weak transcription	Brain Germinal Matrix	brain
47	chr2:136364200-136382000	Weak transcription	Fetal Stomach	stomach
48	chr2:136364200-136382400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:136364200-136394600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:136364200-136394600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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