Variant report

Variant	rs12420456
Chromosome Location	chr11:64981837-64981838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64981666..64983514-chr11:65194659..65196523,2	K562	blood:
2	chr11:64981438..64983077-chr11:65020117..65022507,2	MCF-7	breast:
3	chr11:64936286..64938198-chr11:64981682..64983744,2	K562	blood:
4	chr11:64981559..64983157-chr11:64987692..64989765,2	MCF-7	breast:
5	chr11:64981702..64983459-chr11:65028915..65031631,2	K562	blood:

Variant related genes	Relation type
ENSG00000014138	Chromatin interaction
ENSG00000197847	Chromatin interaction
ENSG00000204710	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11605576	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605632	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12416930	0.83[ASN][1000 genomes]
rs12417272	0.88[ASN][1000 genomes]
rs12420069	0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs17583	0.90[JPT][hapmap]
rs17881590	0.90[ASN][1000 genomes]
rs2271448	0.92[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes]
rs2277307	0.90[JPT][hapmap]
rs34007842	0.82[ASN][1000 genomes]
rs3782093	0.92[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs3825072	0.90[JPT][hapmap]
rs3953797	0.90[JPT][hapmap]
rs58858596	0.84[ASN][1000 genomes]
rs67698652	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12420456	SLC22A24	cis	cerebellum	SCAN
rs12420456	HRASLS2	cis	parietal	SCAN
rs12420456	FIBP	cis	cerebellum	SCAN
rs12420456	CLCF1	cis	parietal	SCAN
rs12420456	PCNXL3	cis	parietal	SCAN
rs12420456	DAGLA	cis	parietal	SCAN
rs12420456	CCDC87	cis	parietal	SCAN
rs12420456	B3GAT3	cis	parietal	SCAN
rs12420456	NUDT8	cis	parietal	SCAN
rs12420456	SCGB1A1	cis	parietal	SCAN
rs12420456	SLC22A20	cis	Esophagus Mucosa	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64950600-64992400	Weak transcription	Right Atrium	heart
2	chr11:64952400-64992800	Weak transcription	Fetal Heart	heart
3	chr11:64973800-64992600	Weak transcription	Fetal Kidney	kidney
4	chr11:64975800-64982400	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:64976600-64992600	Weak transcription	Psoas Muscle	Psoas
6	chr11:64977400-64998400	Weak transcription	Small Intestine	intestine
7	chr11:64977600-64993200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:64978200-64982800	Weak transcription	Fetal Lung	lung
9	chr11:64978200-64986800	Weak transcription	HepG2	liver
10	chr11:64978400-64992200	Weak transcription	Stomach Mucosa	stomach
11	chr11:64978400-64992800	Weak transcription	HSMM	muscle
12	chr11:64978600-64992800	Weak transcription	HSMMtube	muscle
13	chr11:64978800-64987000	Weak transcription	NHDF-Ad	bronchial
14	chr11:64979200-64983000	Weak transcription	Brain Anterior Caudate	brain
15	chr11:64979200-64983400	Enhancers	Primary hematopoietic stem cells	blood
16	chr11:64979200-64986400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:64979200-64987000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:64979200-64992400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:64979200-64993000	Weak transcription	Aorta	Aorta
20	chr11:64979400-64982200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr11:64979400-64984400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:64979400-64987000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:64979400-64992400	Weak transcription	A549	lung
24	chr11:64979600-64984800	Weak transcription	Fetal Brain Female	brain
25	chr11:64979600-64986400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:64979600-64990600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:64979600-64992200	Weak transcription	NHEK	skin
28	chr11:64979800-64982200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:64979800-64983200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:64979800-64984800	Weak transcription	Brain Germinal Matrix	brain
31	chr11:64979800-64984800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:64979800-64989800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:64979800-64992400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:64979800-64993000	Weak transcription	Ovary	ovary
35	chr11:64980000-64982000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr11:64980000-64982200	Enhancers	Fetal Thymus	thymus
37	chr11:64980000-64983400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr11:64980000-64986000	Weak transcription	Lung	lung
39	chr11:64980000-64989800	Weak transcription	Left Ventricle	heart
40	chr11:64980000-64992200	Weak transcription	HMEC	breast
41	chr11:64980200-64982000	Enhancers	Fetal Muscle Trunk	muscle
42	chr11:64980200-64982200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr11:64980200-64982200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:64980200-64982200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:64980200-64982400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr11:64980200-64982600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr11:64980200-64984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:64980200-64992200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:64980200-64992600	Weak transcription	Colonic Mucosa	Colon
50	chr11:64980200-64993000	Weak transcription	Gastric	stomach

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