Variant report

Variant	rs2419772
Chromosome Location	chr11:32872273-32872274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10454479	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10767973	1.00[JPT][hapmap]
rs10835955	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs10835996	1.00[AFR][1000 genomes]
rs10835997	1.00[AFR][1000 genomes]
rs11031928	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11031939	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs11031949	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs11031951	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs11031952	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs11031975	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11031978	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11031981	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11031994	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11031999	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11032000	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11032017	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11032026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032043	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11032058	1.00[AFR][1000 genomes]
rs11032060	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs11032071	1.00[AFR][1000 genomes]
rs11032072	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs11032073	1.00[AFR][1000 genomes]
rs11032074	1.00[JPT][hapmap]
rs11032076	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs1396994	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs174747	1.00[JPT][hapmap]
rs197702	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197703	0.95[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs197706	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs197708	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197711	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2143572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179644	1.00[ASN][1000 genomes]
rs2419773	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664693	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2746036	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs2746037	1.00[JPT][hapmap]
rs2786800	1.00[JPT][hapmap]
rs2900979	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900980	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34991296	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35529733	1.00[AFR][1000 genomes]
rs4755451	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4755455	0.83[EUR][1000 genomes]
rs4755476	1.00[JPT][hapmap]
rs4756328	0.83[EUR][1000 genomes]
rs4756373	1.00[JPT][hapmap]
rs4756385	1.00[JPT][hapmap]
rs6484610	1.00[JPT][hapmap]
rs652963	1.00[JPT][hapmap]
rs7101848	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7104368	1.00[JPT][hapmap]
rs7109323	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7113870	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7124151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128509	1.00[JPT][hapmap]
rs7395190	1.00[JPT][hapmap]
rs7481878	1.00[JPT][hapmap]
rs761284	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs761285	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7931061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935374	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7944318	1.00[JPT][hapmap]
rs7950261	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs960554	1.00[LWK][hapmap]
rs9943506	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2757434	chr11:32792784-32958609	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv34742	chr11:32796092-33004024	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv897190	chr11:32801921-32951836	Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv897191	chr11:32805169-32903263	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv897192	chr11:32828760-32903263	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv897193	chr11:32838288-32903263	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2419772	PRRG4	Cis_1M	lymphoblastoid	RTeQTL
rs2419772	C11orf46	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32852200-32876800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:32852800-32878800	Weak transcription	Placenta	Placenta
3	chr11:32853000-32877200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:32855000-32876800	Weak transcription	Esophagus	oesophagus
5	chr11:32858600-32873800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:32861200-32873400	Weak transcription	NHEK	skin
7	chr11:32862400-32873600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:32862400-32873600	Weak transcription	Hela-S3	cervix
9	chr11:32863200-32873800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:32866000-32874800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:32866000-32878200	Weak transcription	HMEC	breast
12	chr11:32867200-32873600	Weak transcription	Fetal Intestine Large	intestine
13	chr11:32867800-32872800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr11:32867800-32873600	Weak transcription	Fetal Intestine Small	intestine
15	chr11:32868200-32873400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:32869000-32878000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:32869200-32875800	Weak transcription	Spleen	Spleen
18	chr11:32870000-32873000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:32870000-32874800	Weak transcription	Liver	Liver
20	chr11:32870800-32873200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:32871800-32874000	Weak transcription	GM12878-XiMat	blood
22	chr11:32872000-32874800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:32872000-32882000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:32872200-32872400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:32872200-32873200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:32872200-32873600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr11:32872200-32882200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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