Variant report

Variant	rs1969578
Chromosome Location	chr4:160283091-160283092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:160279549..160283118-chr4:160285686..160287785,3	MCF-7	breast:
2	chr4:160274137..160276479-chr4:160281764..160285889,4	K562	blood:
3	chr4:160274137..160276051-chr4:160282977..160285281,2	K562	blood:
4	chr4:160282094..160284235-chr4:160295172..160296934,2	K562	blood:
5	chr4:160282232..160283919-chr4:160283974..160285950,2	K562	blood:

Variant related genes	Relation type
ENSG00000248552	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];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11723634	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.85[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];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13110592	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13115272	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127789	0.96[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13131141	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]
rs13147632	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749465	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6536412	0.83[AMR][1000 genomes];0.86[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
rs1969578	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL
rs1969578	RAPGEF2	cis	normal skin	skin_eQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160237000-160284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:160250000-160283400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:160250000-160284400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:160250400-160285200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:160250800-160284600	Strong transcription	Liver	Liver
6	chr4:160258000-160283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:160264600-160283200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:160264600-160284800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:160266800-160287600	Weak transcription	Psoas Muscle	Psoas
10	chr4:160271000-160286400	Weak transcription	Small Intestine	intestine
11	chr4:160271600-160283600	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:160271600-160284200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:160272000-160283200	Strong transcription	Primary T cells from cord blood	blood
14	chr4:160274200-160289800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:160275000-160283200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:160275200-160287800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:160275200-160303800	Weak transcription	Right Atrium	heart
18	chr4:160275400-160288000	Weak transcription	A549	lung
19	chr4:160276800-160283600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:160279600-160283400	Weak transcription	Ovary	ovary
21	chr4:160280200-160284800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:160280200-160286400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:160280200-160289800	Weak transcription	Spleen	Spleen
24	chr4:160280200-160290800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:160280200-160295200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:160280400-160283600	Weak transcription	Fetal Stomach	stomach
27	chr4:160280400-160286400	Weak transcription	Fetal Intestine Small	intestine
28	chr4:160280600-160283400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:160280600-160283400	Weak transcription	Thymus	Thymus
30	chr4:160280600-160283600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:160280600-160286200	Weak transcription	Esophagus	oesophagus
32	chr4:160280600-160286200	Weak transcription	Gastric	stomach
33	chr4:160280600-160288000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:160280600-160288200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:160280600-160290200	Weak transcription	Pancreas	Pancrea
36	chr4:160280800-160283800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:160280800-160285400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr4:160280800-160286800	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:160280800-160287400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:160280800-160287600	Weak transcription	HepG2	liver
41	chr4:160280800-160288000	Weak transcription	Left Ventricle	heart
42	chr4:160280800-160288200	Weak transcription	Fetal Thymus	thymus
43	chr4:160280800-160288200	Weak transcription	HSMMtube	muscle
44	chr4:160280800-160289600	Weak transcription	Lung	lung
45	chr4:160281200-160288000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr4:160281200-160288000	Weak transcription	Brain Anterior Caudate	brain
47	chr4:160281200-160288000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:160281200-160288200	Weak transcription	GM12878-XiMat	blood
49	chr4:160281200-160292000	Weak transcription	Brain Germinal Matrix	brain
50	chr4:160281800-160283400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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