Variant report

Variant	rs9652567
Chromosome Location	chr15:83368514-83368515
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr15:83368487-83368903	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:83368196-83369008	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr15:83368450-83368862	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:83368422-83368712	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83366323..83369466-chr15:83375659..83378922,4	K562	blood:
2	chr15:83366884..83369469-chr15:83380434..83383177,2	MCF-7	breast:
3	chr15:83241058..83243039-chr15:83367492..83370195,2	K562	blood:
4	chr15:83353470..83356026-chr15:83368438..83370517,2	MCF-7	breast:
5	chr15:83366312..83369718-chr15:83416708..83419690,4	MCF-7	breast:

No data

Variant related genes	Relation type
AP3B2	TF binding region
ENSG00000214575	Chromatin interaction
ENSG00000228141	Chromatin interaction
ENSG00000250988	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10400906	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10468217	0.82[ASN][1000 genomes]
rs10906984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1145172	0.90[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs1145173	0.90[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs11631963	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633829	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11635624	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11637433	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11855735	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12148332	0.84[ASN][1000 genomes]
rs12438312	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12438334	0.81[AFR][1000 genomes]
rs12442686	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259180	0.83[ASN][1000 genomes]
rs1259182	0.87[ASN][1000 genomes]
rs1259183	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1267657	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1267658	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1267659	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1269134	0.88[ASN][1000 genomes]
rs12911134	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916980	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1313492	0.86[ASN][1000 genomes]
rs1313493	0.86[ASN][1000 genomes]
rs1367841	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1594511	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17158390	0.90[ASN][1000 genomes]
rs1864699	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2099259	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2278355	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]
rs2567635	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2567636	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2678445	0.82[ASN][1000 genomes]
rs2678448	0.84[ASN][1000 genomes]
rs28374463	0.86[ASN][1000 genomes]
rs28415133	0.84[ASN][1000 genomes]
rs28595450	0.81[AFR][1000 genomes]
rs28667458	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2870965	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2870966	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28808991	0.86[ASN][1000 genomes]
rs34186444	0.90[ASN][1000 genomes]
rs35934048	0.83[ASN][1000 genomes]
rs36109438	0.84[ASN][1000 genomes]
rs3970696	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4778686	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4779032	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4779039	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4779041	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4779044	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4779053	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4779054	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55924160	0.90[ASN][1000 genomes]
rs57181760	0.88[ASN][1000 genomes]
rs6603033	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698500	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7165125	0.88[ASN][1000 genomes]
rs7166248	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7167880	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7171180	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7178350	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181761	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7182403	0.89[ASN][1000 genomes]
rs7183881	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7494860	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7496954	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783520	0.88[ASN][1000 genomes]
rs783521	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs783522	0.90[ASN][1000 genomes]
rs783523	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs783525	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs783526	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs783527	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs783529	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs783530	0.84[ASN][1000 genomes]
rs783531	0.84[ASN][1000 genomes]
rs783532	0.85[ASN][1000 genomes]
rs783533	0.86[ASN][1000 genomes]
rs783534	0.86[ASN][1000 genomes]
rs783535	0.84[ASN][1000 genomes]
rs783536	0.86[ASN][1000 genomes]
rs783537	0.82[ASN][1000 genomes]
rs783539	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs783540	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs783543	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs783545	0.82[ASN][1000 genomes]
rs803747	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8040293	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8043401	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][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	nsv904450	chr15:83347193-83395340	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9652567	FLJ40113///LOC161527///LOC440295///LOC642346	N/A	lymphoblastoid	RTeQTL
rs9652567	RP11-152F13.8	cis	Esophagus Mucosa	GTEx
rs9652567	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs9652567	LOC402057///RPS17	trans	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83349800-83377200	Weak transcription	Brain Anterior Caudate	brain
2	chr15:83350400-83369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:83350400-83372800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:83350600-83369000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:83351600-83377200	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:83351800-83377200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:83351800-83377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:83355600-83368600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:83357800-83368800	Weak transcription	Brain Angular Gyrus	brain
10	chr15:83358200-83377200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:83363000-83370400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:83364200-83369000	Strong transcription	Fetal Brain Female	brain
13	chr15:83365200-83371000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:83365400-83376600	Weak transcription	Fetal Brain Male	brain
15	chr15:83366400-83369000	Strong transcription	Brain Germinal Matrix	brain
16	chr15:83367400-83368800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:83367600-83369200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:83367600-83370000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:83367600-83370200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:83367800-83368600	Strong transcription	Brain Cingulate Gyrus	brain
21	chr15:83368000-83369000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:83368200-83368600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:83368200-83369000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:83368200-83369200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:83368400-83369200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr15:83368400-83369200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr15:83368400-83376800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:83368400-83377400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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