Variant report

Variant	rs2278355
Chromosome Location	chr15:83331155-83331156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83328672..83331748-chr15:83346249..83349279,3	MCF-7	breast:
2	chr15:83329409..83331309-chr15:83337250..83339534,2	K562	blood:
3	chr15:83330156..83333342-chr15:83346386..83350515,4	MCF-7	breast:
4	chr15:83315603..83319675-chr15:83327659..83331605,4	K562	blood:
5	chr15:83330561..83333118-chr15:83349292..83351934,2	K562	blood:

Variant related genes	Relation type
ENSG00000259462	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10400906	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10468217	0.87[ASN][1000 genomes]
rs10906984	0.82[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1145172	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1145173	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11631963	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633829	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs11635624	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs11637433	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11855735	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs12148332	0.89[ASN][1000 genomes]
rs12438312	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12442686	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1259180	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1259182	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1259183	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267657	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs1267658	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs1267659	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs1269134	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911134	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12916980	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs1313492	0.91[ASN][1000 genomes]
rs1313493	0.91[ASN][1000 genomes]
rs1367841	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs1594511	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17158390	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864699	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099259	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs2567635	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs2567636	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2678445	0.84[ASN][1000 genomes]
rs2678448	0.89[ASN][1000 genomes]
rs28374463	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28415133	0.88[ASN][1000 genomes]
rs28667458	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2870965	0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2870966	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28808991	0.90[ASN][1000 genomes]
rs34186444	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35934048	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36109438	0.88[ASN][1000 genomes]
rs3970696	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.89[ASN][1000 genomes]
rs4778686	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4779032	0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs4779039	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs4779041	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs4779044	0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4779050	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4779053	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4779054	0.86[AFR][1000 genomes]
rs55924160	0.94[ASN][1000 genomes]
rs57181760	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6603033	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs698500	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165125	0.92[ASN][1000 genomes]
rs7166248	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7167880	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs7171180	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs7178350	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7181761	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7182403	0.94[ASN][1000 genomes]
rs7183881	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7494860	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7496954	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs783520	0.93[ASN][1000 genomes]
rs783521	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs783522	0.94[ASN][1000 genomes]
rs783523	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs783525	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs783526	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs783527	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs783529	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs783530	0.89[ASN][1000 genomes]
rs783531	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs783532	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs783533	0.91[ASN][1000 genomes]
rs783534	0.91[ASN][1000 genomes]
rs783535	0.88[ASN][1000 genomes]
rs783536	0.90[ASN][1000 genomes]
rs783537	0.87[ASN][1000 genomes]
rs783539	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs783540	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs783543	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs783545	0.87[ASN][1000 genomes]
rs803686	0.81[GIH][hapmap]
rs803687	0.81[ASN][1000 genomes]
rs803688	0.83[ASN][1000 genomes]
rs803747	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs8040293	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8043401	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9652567	0.86[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	esv18367	chr15:83327137-83332372	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2278355	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs2278355	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL
rs2278355	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs2278355	RP11-152F13.8	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83317200-83331800	Weak transcription	Gastric	stomach
2	chr15:83317200-83336200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:83324800-83331400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:83325800-83333800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:83326600-83336000	Strong transcription	Brain Germinal Matrix	brain
6	chr15:83327800-83337400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:83328200-83331800	Weak transcription	Brain Anterior Caudate	brain
8	chr15:83328800-83331200	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:83328800-83331600	Weak transcription	Fetal Brain Female	brain
10	chr15:83328800-83332400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:83328800-83342600	Weak transcription	Brain Substantia Nigra	brain
12	chr15:83330400-83331400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr15:83330400-83331400	Enhancers	Fetal Brain Male	brain
14	chr15:83331000-83331800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:83331000-83332200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:83331000-83332600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:83331000-83334200	Weak transcription	Brain Angular Gyrus	brain

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