Variant report

Variant	rs6581450
Chromosome Location	chr12:62861111-62861112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62859264..62862504-chr12:62994446..62997723,4	K562	blood:
2	chr12:62860603..62862408-chr12:62877064..62881508,4	MCF-7	breast:
3	chr12:62859326..62863326-chr12:62876630..62881311,5	K562	blood:
4	chr12:62652867..62655436-chr12:62859516..62862606,3	MCF-7	breast:
5	chr12:62859286..62861275-chr12:62995759..62997449,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199179	Chromatin interaction
ENSG00000198673	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000135655	Chromatin interaction
ENSG00000221949	Chromatin interaction
ENSG00000257568	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10161203	0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs10735906	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747964	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747967	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784298	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784300	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615669	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11832508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12298863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498714	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1603823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029938	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173086	0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs4025987	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763022	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4763023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763167	0.81[MEX][hapmap]
rs4763171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132677	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132765	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135893	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136794	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298046	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7303357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7953380	0.81[CHD][hapmap];0.81[MEX][hapmap]
rs7954432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963346	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7963544	0.95[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964563	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965248	0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs7968424	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7970112	0.81[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs7978740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924169	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62859400-62861800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr12:62859400-62862600	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:62859400-62863600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:62859600-62861200	Active TSS	Adipose Nuclei	Adipose
5	chr12:62859600-62861200	Active TSS	Brain Anterior Caudate	brain
6	chr12:62859600-62861400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:62859600-62861400	Active TSS	Brain Cingulate Gyrus	brain
8	chr12:62859600-62861400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:62859600-62861400	Active TSS	Fetal Brain Male	brain
10	chr12:62859600-62861400	Active TSS	Fetal Kidney	kidney
11	chr12:62859600-62861400	Active TSS	Fetal Lung	lung
12	chr12:62859600-62861400	Active TSS	Thymus	Thymus
13	chr12:62859600-62861600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:62859600-62861600	Active TSS	Brain Angular Gyrus	brain
15	chr12:62859600-62861600	Active TSS	Brain Substantia Nigra	brain
16	chr12:62859600-62861600	Active TSS	Fetal Muscle Leg	muscle
17	chr12:62859600-62861800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr12:62859600-62862000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:62859600-62862000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:62859600-62862000	Active TSS	Fetal Muscle Trunk	muscle
21	chr12:62859600-62862200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:62859600-62862200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:62859600-62862200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:62859600-62862200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:62859600-62862200	Active TSS	Aorta	Aorta
26	chr12:62859600-62862200	Active TSS	Right Ventricle	heart
27	chr12:62859600-62862600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr12:62859600-62862600	Active TSS	Fetal Intestine Large	intestine
29	chr12:62859600-62862600	Active TSS	Ovary	ovary
30	chr12:62859600-62862600	Active TSS	NH-A	brain
31	chr12:62859600-62863000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:62859600-62863200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:62859600-62863200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr12:62859800-62861200	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr12:62859800-62861200	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:62859800-62861200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:62859800-62861400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr12:62859800-62861400	Active TSS	Fetal Heart	heart
39	chr12:62859800-62861600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:62859800-62861600	Active TSS	Esophagus	oesophagus
41	chr12:62859800-62861600	Active TSS	Rectal Smooth Muscle	rectum
42	chr12:62859800-62861800	Active TSS	H1 Cell Line	embryonic stem cell
43	chr12:62859800-62861800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr12:62859800-62861800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:62859800-62861800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:62859800-62861800	Active TSS	Colonic Mucosa	Colon
47	chr12:62859800-62861800	Active TSS	Psoas Muscle	Psoas
48	chr12:62859800-62861800	Active TSS	HSMMtube	muscle
49	chr12:62859800-62862000	Active TSS	Colon Smooth Muscle	Colon
50	chr12:62859800-62862000	Active TSS	Placenta	Placenta

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