Variant report

Variant	rs12503790
Chromosome Location	chr4:160179113-160179114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11100211	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11730876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502799	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507531	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508599	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509160	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12509165	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13116575	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13119443	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13124646	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13152231	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56806866	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6536402	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67377365	0.88[EUR][1000 genomes]
rs7659528	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9992208	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12503790	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160160600-160179800	Weak transcription	NHEK	skin
3	chr4:160167400-160186400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:160169800-160187800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:160170000-160187200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:160170200-160188000	Weak transcription	Fetal Kidney	kidney
7	chr4:160170400-160180000	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:160170400-160183200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:160170400-160186400	Weak transcription	Fetal Brain Male	brain
10	chr4:160170400-160188000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:160170400-160188400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:160170400-160192800	Weak transcription	Primary T cells from cord blood	blood
13	chr4:160170600-160180000	Weak transcription	Brain Angular Gyrus	brain
14	chr4:160170600-160183200	Weak transcription	NHDF-Ad	bronchial
15	chr4:160170600-160188000	Weak transcription	Osteobl	bone
16	chr4:160170600-160188200	Weak transcription	Psoas Muscle	Psoas
17	chr4:160171200-160183200	Weak transcription	Brain Anterior Caudate	brain
18	chr4:160172600-160182800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:160172600-160182800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:160172600-160188200	Weak transcription	Pancreas	Pancrea
21	chr4:160172600-160193000	Weak transcription	Gastric	stomach
22	chr4:160173000-160193200	Weak transcription	Thymus	Thymus
23	chr4:160173200-160179800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:160173200-160183400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:160173200-160187800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:160173200-160188200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:160173200-160188600	Weak transcription	Lung	lung
28	chr4:160173200-160192400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:160173400-160188000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:160173400-160188000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:160173400-160188000	Weak transcription	Fetal Stomach	stomach
33	chr4:160173400-160188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:160173400-160188200	Weak transcription	Right Ventricle	heart
35	chr4:160173400-160188400	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:160173400-160188400	Weak transcription	GM12878-XiMat	blood
37	chr4:160173400-160188400	Weak transcription	HSMM	muscle
38	chr4:160173400-160192600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:160173400-160194000	Weak transcription	Fetal Intestine Large	intestine
40	chr4:160173400-160194800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:160173600-160181200	Weak transcription	Left Ventricle	heart
42	chr4:160173600-160188400	Weak transcription	Fetal Intestine Small	intestine
43	chr4:160173800-160180400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:160174000-160203400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:160174200-160179800	Weak transcription	Brain Substantia Nigra	brain
46	chr4:160174400-160181600	Weak transcription	Fetal Lung	lung
47	chr4:160174400-160182800	Weak transcription	HUVEC	blood vessel
48	chr4:160174400-160183200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:160174400-160183400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:160174600-160179800	Weak transcription	Brain Cingulate Gyrus	brain

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