Variant report

Variant	rs7938820
Chromosome Location	chr11:17077452-17077453
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	chr11:17076833..17079491-chr11:17096981..17099134,2	K562	blood:

Variant related genes	Relation type
ENSG00000110700	Chromatin interaction
ENSG00000201403	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10766373	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832727	0.83[ASN][1000 genomes]
rs10832728	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10832733	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10832734	0.82[AMR][1000 genomes]
rs10832735	0.80[AMR][1000 genomes]
rs10832736	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10832739	0.81[AFR][1000 genomes]
rs10832747	0.86[CEU][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap]
rs11024113	0.86[ASN][1000 genomes]
rs11024116	0.86[ASN][1000 genomes]
rs11024130	0.83[ASN][1000 genomes]
rs11024131	0.83[ASN][1000 genomes]
rs11024143	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11024148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024158	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap]
rs11024159	0.83[AFR][1000 genomes]
rs11024163	0.81[AFR][1000 genomes]
rs11024204	0.94[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs11821773	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12280930	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs12286505	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs12293395	0.85[ASN][1000 genomes]
rs1236309	0.82[AFR][1000 genomes]
rs17472886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214900	0.94[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap]
rs214901	0.94[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs214906	0.81[AFR][1000 genomes]
rs214910	0.94[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap]
rs214914	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs214925	0.94[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs214927	0.92[CEU][hapmap];0.88[YRI][hapmap]
rs214935	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs214936	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap]
rs214939	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs214940	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap]
rs34591697	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35933265	0.83[AMR][1000 genomes]
rs4255517	0.86[ASN][1000 genomes]
rs4356203	0.89[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4456241	0.86[ASN][1000 genomes]
rs4517490	0.86[ASN][1000 genomes]
rs512852	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs550667	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs603618	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs615358	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs618331	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6486346	0.85[ASN][1000 genomes]
rs6486347	0.83[ASN][1000 genomes]
rs6486348	0.85[ASN][1000 genomes]
rs6486352	0.82[AFR][1000 genomes]
rs677540	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap]
rs7104247	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71047522	0.85[ASN][1000 genomes]
rs7106705	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7106954	0.85[ASN][1000 genomes]
rs7107283	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7107745	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7118006	0.80[AFR][1000 genomes]
rs7123301	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7125607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7396382	0.81[AFR][1000 genomes]
rs7396958	0.82[AFR][1000 genomes]
rs7478986	0.96[CEU][hapmap]
rs7925692	0.83[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap]
rs7927240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929927	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs7930058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7932916	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935219	0.82[AFR][1000 genomes]
rs7937770	0.84[AMR][1000 genomes]
rs7937880	0.85[ASN][1000 genomes]
rs7939614	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7939750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7946165	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949405	0.85[ASN][1000 genomes]
rs7949699	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7950225	0.83[ASN][1000 genomes]
rs9919540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9919600	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][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	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv971988	chr11:17068362-17084978	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7938820	SAA4	cis	parietal	SCAN
rs7938820	PDE3B	cis	parietal	SCAN
rs7938820	NUCB2	cis	multi-tissue	Pritchard
rs7938820	SPTY2D1	cis	parietal	SCAN
rs7938820	SERGEF	cis	parietal	SCAN
rs7938820	OR7E14P	cis	Nerve Tibial	GTEx
rs7938820	OR7E14P	cis	Esophagus Mucosa	GTEx
rs7938820	RNU14	cis	multi-tissue	Pritchard
rs7938820	NUCB2	cis	lymphoblastoid	seeQTL
rs7938820	NUCB2	cis	cerebellum	SCAN
rs7938820	NUCB2	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17069400-17096200	Weak transcription	Pancreas	Pancrea
2	chr11:17070600-17088400	Weak transcription	Fetal Intestine Small	intestine

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