Variant report

Variant	rs1140886
Chromosome Location	chr12:121681536-121681537
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	chr12:121674738..121676448-chr12:121680498..121682374,2	MCF-7	breast:
2	chr12:121676166..121678548-chr12:121679208..121682170,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1063843	0.85[MEX][hapmap];0.85[AMR][1000 genomes]
rs1653591	0.93[LWK][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes]
rs2668247	0.81[AMR][1000 genomes]
rs2686340	0.82[AMR][1000 genomes]
rs2686342	0.85[MEX][hapmap];0.85[AMR][1000 genomes]
rs2686344	0.93[LWK][hapmap];0.85[MKK][hapmap];0.82[AMR][1000 genomes]
rs2686345	0.93[LWK][hapmap];0.85[MKK][hapmap];0.82[AMR][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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv455731	chr12:121668254-121687174	Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv560456	chr12:121668254-121687174	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1140886	POP5	cis	parietal	SCAN
rs1140886	ACADS	cis	parietal	SCAN
rs1140886	KDM2B	cis	cerebellum	SCAN
rs1140886	GPR109B	cis	cerebellum	SCAN
rs1140886	MLXIP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
2	chr12:121662800-121690600	Weak transcription	Fetal Brain Male	brain
3	chr12:121667800-121685200	Weak transcription	Hela-S3	cervix
4	chr12:121670200-121689400	Strong transcription	Fetal Brain Female	brain
5	chr12:121670600-121695000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:121671200-121686200	Weak transcription	Small Intestine	intestine
7	chr12:121674400-121687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:121674600-121692800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:121674600-121704200	Strong transcription	Brain Germinal Matrix	brain
10	chr12:121676800-121684800	Weak transcription	Stomach Mucosa	stomach
11	chr12:121677400-121686800	Weak transcription	HUVEC	blood vessel
12	chr12:121677400-121688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:121677400-121695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:121677400-121717000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:121677400-121717200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:121677600-121688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:121678600-121690400	Weak transcription	Psoas Muscle	Psoas
18	chr12:121678800-121682600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:121679000-121713000	Strong transcription	Fetal Intestine Large	intestine
20	chr12:121679200-121681600	Weak transcription	Aorta	Aorta
21	chr12:121679200-121685000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:121679200-121709200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:121679200-121714400	Weak transcription	Right Atrium	heart
24	chr12:121679400-121683000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:121679400-121699000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:121679400-121713800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:121679600-121682000	Strong transcription	Brain Anterior Caudate	brain
28	chr12:121679600-121682600	Weak transcription	Colonic Mucosa	Colon
29	chr12:121679600-121684200	Strong transcription	Lung	lung
30	chr12:121679600-121685000	Weak transcription	GM12878-XiMat	blood
31	chr12:121679600-121685200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:121679600-121685800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:121679600-121686000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:121679600-121687000	Weak transcription	NHEK	skin
35	chr12:121679600-121688400	Weak transcription	HSMM	muscle
36	chr12:121679600-121690800	Weak transcription	K562	blood
37	chr12:121679600-121708800	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:121679600-121709200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr12:121679600-121713000	Strong transcription	Liver	Liver
40	chr12:121679600-121732600	Strong transcription	Fetal Intestine Small	intestine
41	chr12:121679800-121681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:121679800-121681600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:121679800-121681600	Weak transcription	Esophagus	oesophagus
44	chr12:121679800-121682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:121679800-121682400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:121679800-121685000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:121679800-121687800	Weak transcription	NHDF-Ad	bronchial
48	chr12:121679800-121690400	Strong transcription	Fetal Stomach	stomach
49	chr12:121679800-121694600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:121679800-121703200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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