Variant report

Variant	rs7163990
Chromosome Location	chr15:83344271-83344272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83343222..83344781-chr15:83348435..83350290,2	K562	blood:
2	chr15:83342701..83346564-chr15:83347481..83349539,4	MCF-7	breast:
3	chr15:83343188..83346700-chr15:83346875..83348889,3	K562	blood:

Variant related genes	Relation type
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10152286	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10468211	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10468219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12324877	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12385960	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12385961	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12437576	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12438371	1.00[GIH][hapmap]
rs12438565	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440776	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441776	1.00[CEU][hapmap]
rs12442733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12443184	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13379712	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17158391	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17158405	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28485966	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59568968	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7162465	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72751690	0.96[AFR][1000 genomes]
rs9806343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806381	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription 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	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS 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	43 gene(s)	inside rSNPs	diseases
11	esv1808975	chr15:83307574-83360168	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7163990	LOC283726	cis	multi-tissue	Pritchard
rs7163990	FAM154B	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83331400-83346600	Weak transcription	Fetal Brain Male	brain
2	chr15:83334800-83344400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:83335200-83349200	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:83336800-83348200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:83340200-83348600	Weak transcription	Pancreas	Pancrea
6	chr15:83340600-83348600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:83341600-83345600	Strong transcription	Brain Germinal Matrix	brain
8	chr15:83342800-83345600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:83342800-83346400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:83342800-83348400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:83343000-83350000	Weak transcription	Brain Substantia Nigra	brain
12	chr15:83343800-83344400	Weak transcription	Brain Anterior Caudate	brain
13	chr15:83344000-83345200	Weak transcription	Fetal Brain Female	brain
14	chr15:83344000-83346600	Strong transcription	Brain Angular Gyrus	brain
15	chr15:83344200-83347200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:83344200-83347800	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr15:83344200-83348800	Weak transcription	Gastric	stomach

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