Variant report

Variant	rs12658
Chromosome Location	chr12:42853084-42853085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:42853053-42853542	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:42853073-42853249	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000257225	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10880301	0.80[GIH][hapmap]
rs12231113	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17091074	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34725377	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7963469	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv983461	chr12:42851064-42854179	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12658	ZCRB1	cis	cerebellum	SCAN
rs12658	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs12658	ZCRB1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42816200-42858200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:42820000-42858200	Weak transcription	Gastric	stomach
4	chr12:42826400-42859000	Weak transcription	Fetal Brain Male	brain
5	chr12:42826600-42858200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
7	chr12:42834200-42859600	Weak transcription	Brain Substantia Nigra	brain
8	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
9	chr12:42836800-42858800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:42837000-42853200	Weak transcription	NHEK	skin
11	chr12:42837000-42853800	Weak transcription	Lung	lung
12	chr12:42837000-42858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:42837000-42858000	Weak transcription	Aorta	Aorta
14	chr12:42837000-42858200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
16	chr12:42837200-42863200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:42838400-42858000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:42838600-42853200	Weak transcription	Brain Anterior Caudate	brain
19	chr12:42840000-42856400	Weak transcription	Fetal Intestine Small	intestine
20	chr12:42840400-42860800	Weak transcription	Colonic Mucosa	Colon
21	chr12:42840600-42858000	Weak transcription	Placenta	Placenta
22	chr12:42840600-42860000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:42840800-42853200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:42840800-42853200	Weak transcription	Fetal Kidney	kidney
25	chr12:42840800-42858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:42841000-42853600	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:42841000-42858600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:42841400-42856400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:42841400-42862000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:42841600-42858400	Weak transcription	Fetal Brain Female	brain
31	chr12:42841600-42862400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:42843000-42853200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:42843000-42862400	Weak transcription	Fetal Thymus	thymus
34	chr12:42843200-42853200	Weak transcription	Ovary	ovary
35	chr12:42843200-42858200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:42843200-42858200	Weak transcription	Pancreas	Pancrea
37	chr12:42843200-42862000	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:42843600-42862400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:42844000-42856400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:42844400-42853200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:42844400-42853200	Weak transcription	NHLF	lung
42	chr12:42844400-42858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:42844800-42862600	Weak transcription	Primary T cells from cord blood	blood
44	chr12:42845000-42853800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:42845000-42857600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:42845200-42856400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:42848200-42853600	Weak transcription	Fetal Intestine Large	intestine
48	chr12:42849400-42864800	Strong transcription	Fetal Stomach	stomach
49	chr12:42850000-42860800	Strong transcription	HSMMtube	muscle
50	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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