Variant report

Variant	rs12532461
Chromosome Location	chr7:38873858-38873859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38873668..38876068-chr7:38880511..38882054,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10242978	0.80[ASN][1000 genomes]
rs10272767	0.80[ASN][1000 genomes]
rs12538785	0.81[EUR][1000 genomes]
rs1473137	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17255994	1.00[LWK][hapmap]
rs1859937	0.81[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs2074656	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2240350	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs2240355	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs2240555	0.84[JPT][hapmap]
rs2286081	0.84[CHB][hapmap]
rs2286095	0.82[CHB][hapmap]
rs2286097	0.84[CHB][hapmap]
rs2286099	0.84[CHB][hapmap]
rs2392609	0.84[JPT][hapmap]
rs2893567	0.80[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3779126	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs3801135	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4430003	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723793	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462862	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs6961672	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs7785161	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7788664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7803397	0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs9638944	0.89[JPT][hapmap]

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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12532461	TBX20	cis	parietal	SCAN
rs12532461	CDK2AP1	trans	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:38863000-38876800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
9	chr7:38863800-38879600	Weak transcription	Fetal Lung	lung
10	chr7:38864000-38874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:38865800-38879600	Weak transcription	Right Atrium	heart
12	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:38866400-38876800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:38866400-38877000	Weak transcription	Primary T cells from cord blood	blood
15	chr7:38866800-38877000	Weak transcription	Primary B cells from cord blood	blood
16	chr7:38867200-38876800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:38867400-38877800	Weak transcription	Fetal Brain Male	brain
18	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
19	chr7:38867600-38879600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:38869600-38888400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr7:38870000-38876600	Weak transcription	GM12878-XiMat	blood
22	chr7:38870000-38888200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:38871000-38884400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:38871400-38880400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
28	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:38871600-38875400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr7:38871600-38878400	Weak transcription	Brain Angular Gyrus	brain
31	chr7:38871600-38879800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:38873200-38876800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:38873200-38884400	Weak transcription	Gastric	stomach
36	chr7:38873200-38889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
38	chr7:38873600-38874000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:38873800-38874200	Enhancers	Colon Smooth Muscle	Colon
40	chr7:38873800-38874400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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