Variant report

Variant	rs13131141
Chromosome Location	chr4:160278585-160278586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:160268447..160272441-chr4:160277985..160281156,3	K562	blood:

Variant related genes	Relation type
ENSG00000109756	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10022399	0.92[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11723634	0.92[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11727094	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13110592	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13115272	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127789	0.96[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13147632	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1969578	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749465	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6536412	0.90[AMR][1000 genomes];0.91[EUR][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	nsv1022771	chr4:160188801-160324683	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13131141	RAPGEF2	cis	normal skin	skin_eQTL
rs13131141	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160237000-160279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:160237000-160284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:160238600-160282200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:160241000-160281600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:160250000-160283400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:160250000-160284400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:160250400-160285200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:160250800-160284600	Strong transcription	Liver	Liver
9	chr4:160258000-160283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:160259000-160279200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:160259000-160279200	Strong transcription	Adipose Nuclei	Adipose
12	chr4:160259000-160282800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:160259000-160282800	Strong transcription	Placenta	Placenta
14	chr4:160259200-160279200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:160259200-160283000	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr4:160259400-160278600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:160259400-160283000	Strong transcription	Fetal Intestine Large	intestine
18	chr4:160259600-160282800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:160260000-160282000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:160261000-160279200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:160261200-160281600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:160264400-160283000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:160264600-160281000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:160264600-160283200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:160264600-160284800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:160266800-160287600	Weak transcription	Psoas Muscle	Psoas
27	chr4:160267400-160282400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:160267800-160282400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:160268800-160282800	Weak transcription	Stomach Mucosa	stomach
30	chr4:160269400-160279200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr4:160269600-160282000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:160270400-160280000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr4:160270600-160283000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:160270800-160281800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:160271000-160279200	Weak transcription	K562	blood
36	chr4:160271000-160286400	Weak transcription	Small Intestine	intestine
37	chr4:160271200-160283000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:160271600-160279200	Strong transcription	Brain Anterior Caudate	brain
39	chr4:160271600-160281800	Strong transcription	Primary hematopoietic stem cells	blood
40	chr4:160271600-160283600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:160271600-160284200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:160271800-160280000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr4:160272000-160280800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:160272000-160281200	Strong transcription	Brain Germinal Matrix	brain
45	chr4:160272000-160282200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:160272000-160282400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr4:160272000-160282600	Strong transcription	Dnd41	blood
48	chr4:160272000-160283200	Strong transcription	Primary T cells from cord blood	blood
49	chr4:160272200-160278600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:160272200-160279400	Strong transcription	Fetal Stomach	stomach

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