Variant report

Variant	rs6488063
Chromosome Location	chr12:32706316-32706317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10431226	0.86[AMR][1000 genomes]
rs10431284	0.89[CHD][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[AMR][1000 genomes]
rs10844237	0.89[CHD][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs10844239	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844240	0.81[ASN][1000 genomes]
rs10844241	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844242	0.86[AMR][1000 genomes]
rs11052063	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11052066	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11052068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1499615	0.81[CHD][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes]
rs1846553	0.82[AMR][1000 genomes]
rs1875059	1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs2088656	0.81[CHD][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes]
rs4931634	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931636	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931637	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5006548	0.87[AMR][1000 genomes]
rs6488062	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488064	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305459	0.89[CHD][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs7964106	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972677	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases
2	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1037224	chr12:32698189-32721994	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv541456	chr12:32698189-32721994	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32693000-32729600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:32698800-32719600	Weak transcription	Colonic Mucosa	Colon
3	chr12:32699600-32714800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:32700000-32711400	Weak transcription	HepG2	liver
5	chr12:32701800-32711400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:32702000-32711200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:32702000-32711400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:32702000-32711400	Weak transcription	NHEK	skin
9	chr12:32702000-32719400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:32702000-32719400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:32702400-32711200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:32702400-32711200	Weak transcription	Esophagus	oesophagus
13	chr12:32702800-32710800	Weak transcription	Liver	Liver
14	chr12:32702800-32711400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:32702800-32717200	Weak transcription	HUVEC	blood vessel
16	chr12:32703000-32707600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:32703000-32708200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:32703000-32711000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:32703000-32711200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:32703000-32711200	Weak transcription	Aorta	Aorta
21	chr12:32703000-32711200	Weak transcription	Pancreas	Pancrea
22	chr12:32703000-32711200	Weak transcription	Right Ventricle	heart
23	chr12:32703000-32711400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:32703000-32711400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:32703000-32711600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:32703000-32717000	Weak transcription	HMEC	breast
27	chr12:32703000-32717200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:32703000-32719400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:32703200-32707800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:32703200-32711000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:32703200-32711000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:32703200-32711200	Weak transcription	Stomach Mucosa	stomach
33	chr12:32703200-32711200	Weak transcription	NHLF	lung
34	chr12:32703200-32719000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:32703400-32711200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:32703400-32711200	Weak transcription	NHDF-Ad	bronchial
37	chr12:32703400-32711600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:32703400-32713000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:32703600-32710800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:32703600-32711600	Weak transcription	HSMMtube	muscle
41	chr12:32703600-32712400	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:32704200-32706800	Weak transcription	Right Atrium	heart
43	chr12:32704200-32707800	Weak transcription	Ovary	ovary
44	chr12:32704200-32710800	Weak transcription	Adipose Nuclei	Adipose
45	chr12:32704200-32711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:32704200-32711600	Weak transcription	Primary B cells from cord blood	blood
47	chr12:32704200-32712800	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:32704200-32712800	Weak transcription	Lung	lung
49	chr12:32704200-32719800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:32704400-32707800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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