Variant report

Variant	rs7247184
Chromosome Location	chr19:40048394-40048395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12608773	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609985	0.95[CEU][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs12610740	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12610751	0.87[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12610833	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12611125	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972285	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12972675	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12973775	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12978311	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12980249	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1368469	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17641650	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs17795475	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1836011	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs34126123	0.86[EUR][1000 genomes]
rs34271968	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34355544	0.85[EUR][1000 genomes]
rs34856311	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34885802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35038530	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35939822	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3746086	0.82[ASN][1000 genomes]
rs4608447	0.81[EUR][1000 genomes]
rs4803258	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803259	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55994613	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59485553	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60587381	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67832846	0.86[EUR][1000 genomes]
rs7247218	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7507648	0.82[EUR][1000 genomes]

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	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv34120	chr19:40044635-40131820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7247184	EID2B	cis	lymphoblastoid	seeQTL
rs7247184	GSK3A	cis	cerebellum	SCAN
rs7247184	SNRPD2	cis	cerebellum	SCAN
rs7247184	DHX34	cis	cerebellum	SCAN
rs7247184	CBLC	cis	parietal	SCAN
rs7247184	MRPS12	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40031200-40049600	Weak transcription	Right Atrium	heart
2	chr19:40044200-40048400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:40044200-40049600	Weak transcription	Spleen	Spleen
4	chr19:40046200-40050800	Enhancers	Placenta	Placenta
5	chr19:40047000-40048400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr19:40047400-40048800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr19:40047600-40050000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr19:40047600-40050000	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr19:40048000-40048400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:40048000-40048400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr19:40048000-40048400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr19:40048000-40048400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr19:40048000-40048400	Enhancers	HepG2	liver
14	chr19:40048000-40048600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr19:40048000-40049000	Enhancers	A549	lung
16	chr19:40048000-40049600	Enhancers	Stomach Mucosa	stomach
17	chr19:40048000-40049800	Enhancers	Fetal Thymus	thymus
18	chr19:40048200-40048400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr19:40048200-40048400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr19:40048200-40048400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:40048200-40048400	Enhancers	Hela-S3	cervix
22	chr19:40048200-40048600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:40048200-40048600	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr19:40048200-40048800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr19:40048200-40048800	Enhancers	Liver	Liver
26	chr19:40048200-40049600	Enhancers	Rectal Smooth Muscle	rectum
27	chr19:40048200-40049800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:40048200-40050000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:40048200-40050000	Flanking Active TSS	GM12878-XiMat	blood

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