Variant report

Variant	rs7965230
Chromosome Location	chr12:21676039-21676040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1060126	0.83[CEU][hapmap];1.00[CHD][hapmap]
rs1061626	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs1061627	0.83[CEU][hapmap];1.00[CHD][hapmap]
rs11046090	1.00[ASN][1000 genomes]
rs11046091	0.83[ASW][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs12312710	0.89[ASW][hapmap];1.00[CHD][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs1558502	1.00[ASN][1000 genomes]
rs16923862	1.00[ASN][1000 genomes]
rs3088178	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3213213	0.94[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60206314	1.00[ASN][1000 genomes]
rs61926330	1.00[ASN][1000 genomes]
rs61926342	1.00[ASN][1000 genomes]
rs67187752	1.00[ASN][1000 genomes]
rs7299256	1.00[ASN][1000 genomes]
rs7307064	1.00[CHD][hapmap]
rs7313618	0.84[ASW][hapmap];1.00[ASN][1000 genomes]
rs7976409	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised 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	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv528556	chr12:21664879-21680363	Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv557743	chr12:21670410-21688900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7965230	GOLT1B	cis	cerebellum	SCAN
rs7965230	PYROXD1	cis	parietal	SCAN
rs7965230	KCNJ8	cis	parietal	SCAN
rs7965230	PYROXD1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
2	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
3	chr12:21656800-21680000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:21657400-21680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:21657600-21679800	Weak transcription	Pancreas	Pancrea
6	chr12:21657600-21680000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:21657600-21680400	Weak transcription	Gastric	stomach
8	chr12:21661400-21677200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:21666000-21680200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:21666800-21676800	Weak transcription	Fetal Brain Female	brain
11	chr12:21666800-21679800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:21666800-21680000	Weak transcription	Psoas Muscle	Psoas
13	chr12:21666800-21680200	Weak transcription	Colonic Mucosa	Colon
14	chr12:21666800-21680400	Weak transcription	Spleen	Spleen
15	chr12:21667000-21680200	Weak transcription	Left Ventricle	heart
16	chr12:21667000-21680200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:21667000-21680200	Weak transcription	HSMMtube	muscle
18	chr12:21667200-21678000	Weak transcription	Lung	lung
19	chr12:21667200-21680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:21667200-21680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:21667200-21680000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:21667600-21680000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:21667600-21680200	Weak transcription	NHLF	lung
24	chr12:21669200-21680000	Weak transcription	HMEC	breast
25	chr12:21669400-21678200	Weak transcription	A549	lung
26	chr12:21669400-21678800	Weak transcription	Hela-S3	cervix
27	chr12:21669400-21679000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:21669400-21680200	Weak transcription	Placenta	Placenta
29	chr12:21669800-21678000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:21669800-21679800	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:21670000-21676600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:21670000-21678000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:21670200-21676400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:21670200-21680000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:21670600-21676200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:21670600-21679600	Weak transcription	Adipose Nuclei	Adipose
37	chr12:21670800-21680000	Weak transcription	Osteobl	bone
38	chr12:21671200-21679200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:21671400-21676200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:21671600-21676400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:21671600-21676600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:21671600-21680000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:21671600-21680000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:21671800-21680000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr12:21672000-21676600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:21672200-21677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:21672200-21679200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:21672400-21676600	Weak transcription	Liver	Liver
49	chr12:21672400-21679800	Weak transcription	NH-A	brain
50	chr12:21672400-21680000	Weak transcription	Stomach Smooth Muscle	stomach

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