Variant report

Variant	rs789722
Chromosome Location	chr12:64519806-64519807
allele	C/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	ZNF263	chr12:64519682-64520241	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64519614..64522178-chr12:64614567..64616218,2	MCF-7	breast:

Variant related genes	Relation type
SRGAP1	TF binding region
ENSG00000243024	Chromatin interaction
ENSG00000174206	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1067637	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747997	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10747998	0.81[EUR][1000 genomes]
rs10878105	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2279666	0.81[CEU][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4763138	0.93[CHD][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131691	0.83[CHD][hapmap]
rs789724	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs789729	0.83[CHB][hapmap];0.80[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs789731	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs789741	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs790193	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs789722	EFCAB2	trans	parietal	SCAN
rs789722	RBMS1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64474800-64521400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:64477400-64520800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:64483000-64521400	Weak transcription	Liver	Liver
4	chr12:64483200-64520800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:64483200-64521400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:64483600-64521400	Weak transcription	Lung	lung
7	chr12:64487400-64526600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:64491800-64523600	Weak transcription	HUVEC	blood vessel
9	chr12:64493200-64523600	Weak transcription	Brain Angular Gyrus	brain
10	chr12:64494000-64521400	Weak transcription	Psoas Muscle	Psoas
11	chr12:64494200-64521400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:64496400-64520800	Weak transcription	Spleen	Spleen
13	chr12:64498400-64538400	Weak transcription	Small Intestine	intestine
14	chr12:64498600-64521400	Weak transcription	NH-A	brain
15	chr12:64499000-64521400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:64503200-64521400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:64504200-64520800	Weak transcription	Right Ventricle	heart
18	chr12:64506200-64521200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:64506400-64521400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:64506600-64527000	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:64506800-64521400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:64506800-64521400	Weak transcription	Fetal Kidney	kidney
23	chr12:64506800-64521400	Weak transcription	Fetal Lung	lung
24	chr12:64506800-64527200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:64510600-64521400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:64510600-64527200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:64510800-64520800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:64511000-64520000	Weak transcription	Fetal Intestine Large	intestine
29	chr12:64511000-64520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:64511000-64520800	Weak transcription	Aorta	Aorta
31	chr12:64511000-64521200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:64511000-64521200	Weak transcription	Brain Germinal Matrix	brain
33	chr12:64511000-64521400	Weak transcription	Fetal Intestine Small	intestine
34	chr12:64511000-64521400	Weak transcription	Fetal Stomach	stomach
35	chr12:64511000-64521400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:64511000-64523400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:64511000-64530200	Weak transcription	Right Atrium	heart
38	chr12:64511200-64539400	Weak transcription	HepG2	liver
39	chr12:64513000-64521400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:64514600-64522400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:64514800-64535800	Weak transcription	Hela-S3	cervix
42	chr12:64515200-64520000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:64516000-64520800	Weak transcription	Brain Anterior Caudate	brain
44	chr12:64516200-64520800	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:64516200-64521400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:64517000-64520200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:64517000-64521400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:64517000-64521800	Strong transcription	NHEK	skin
49	chr12:64518000-64520200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:64518000-64527200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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