Variant report

Variant	rs12369961
Chromosome Location	chr12:62966584-62966585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62960289..62962164-chr12:62965214..62967801,2	MCF-7	breast:
2	chr12:62964193..62966992-chr12:62967473..62969692,2	MCF-7	breast:
3	chr12:62956004..62957777-chr12:62965289..62967550,2	K562	blood:
4	chr12:62965202..62967572-chr12:62967863..62969562,2	K562	blood:
5	chr12:62859129..62860829-chr12:62965215..62967388,2	MCF-7	breast:
6	chr12:62964718..62966702-chr12:62967863..62969390,2	K562	blood:

Variant related genes	Relation type
ENSG00000061987	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10877855	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877856	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877857	0.88[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877859	0.88[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877862	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877864	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877870	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174487	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11174494	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174495	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174496	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11174498	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174504	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174514	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174517	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174518	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174527	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174537	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11174557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11174562	0.91[AFR][1000 genomes]
rs11174568	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174569	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174571	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174575	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11174576	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11520127	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11613132	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11614022	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11614822	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12367878	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12369751	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12369985	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12370404	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12580567	1.00[CHB][hapmap]
rs17731893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs17732089	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17732182	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2270732	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55833440	0.91[AFR][1000 genomes]
rs7296573	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7297093	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7301016	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7302094	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7302456	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7303825	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7311952	1.00[JPT][hapmap]
rs73124315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73126004	0.91[AFR][1000 genomes]
rs73126024	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73141014	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73141045	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7962519	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7975109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:62915800-62971600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
4	chr12:62919800-62970000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:62924400-62969800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:62924800-62967600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:62927400-62967400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:62938000-62995400	Weak transcription	Stomach Mucosa	stomach
10	chr12:62944600-62989000	Weak transcription	Colonic Mucosa	Colon
11	chr12:62950200-62966800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:62950400-62995600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:62950600-62975000	Weak transcription	Right Ventricle	heart
14	chr12:62950600-62982600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:62950600-62991200	Weak transcription	Gastric	stomach
16	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
17	chr12:62950800-62968200	Weak transcription	Aorta	Aorta
18	chr12:62950800-62987600	Weak transcription	Pancreas	Pancrea
19	chr12:62950800-62995000	Weak transcription	NHEK	skin
20	chr12:62951000-62987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:62951200-62971600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:62951200-62979600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:62951200-62986800	Weak transcription	Brain Angular Gyrus	brain
25	chr12:62951200-62988600	Weak transcription	Spleen	Spleen
26	chr12:62951200-62995200	Weak transcription	Hela-S3	cervix
27	chr12:62951200-62995600	Weak transcription	HSMMtube	muscle
28	chr12:62951400-62995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:62953400-62996000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:62954800-62989000	Weak transcription	Lung	lung
31	chr12:62954800-62995600	Weak transcription	Brain Anterior Caudate	brain
32	chr12:62955000-62968000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:62955000-62987800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:62955200-62995200	Weak transcription	HepG2	liver
35	chr12:62955600-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:62957000-62995600	Weak transcription	Fetal Brain Male	brain
37	chr12:62957200-62972400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:62957200-62995600	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:62958600-62966600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:62958600-62966600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr12:62958600-62966600	Strong transcription	Adipose Nuclei	Adipose
42	chr12:62958600-62969000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:62958600-62969600	Strong transcription	Fetal Thymus	thymus
44	chr12:62958600-62970000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:62958600-62970400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:62958600-62972800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:62958600-62972800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:62958800-62969200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:62958800-62970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:62959000-62967400	Strong transcription	Primary B cells from cord blood	blood

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