Variant report

Variant	rs10089520
Chromosome Location	chr8:11686089-11686090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:11685829-11686119	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:11685880-11686216	H1-hESC	embryonic stem cell:	n/a	n/a
3	PML	chr8:11684221-11686499	K562	blood:	n/a	n/a
4	POLR2A	chr8:11685646-11686621	HL-60	blood:	n/a	n/a
5	TEAD4	chr8:11685631-11686244	K562	blood:	n/a	n/a
6	CHD2	chr8:11685850-11686667	K562	blood:	n/a	n/a
7	POLR2A	chr8:11684804-11686459	K562	blood:	n/a	n/a
8	POLR2A	chr8:11685836-11686611	HepG2	liver:	n/a	n/a
9	POLR2A	chr8:11685798-11686327	HepG2	liver:	n/a	n/a
10	POLR2A	chr8:11676833-11707731	K562	blood:	n/a	n/a
11	POLR2A	chr8:11684071-11686673	K562	blood:	n/a	n/a
12	POLR2A	chr8:11685786-11686176	K562	blood:	n/a	n/a
13	POLR2A	chr8:11685143-11686492	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr8:11685789-11686218	HepG2	liver:	n/a	n/a
15	POLR2A	chr8:11685844-11686442	HepG2	liver:	n/a	n/a
16	CTCF	chr8:11686080-11686230	AG04449	skin:	n/a	n/a
17	POLR2A	chr8:11685887-11686143	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr8:11685133-11686613	HepG2	liver:	n/a	n/a
19	POLR2A	chr8:11685669-11686264	HL-60	blood:	n/a	n/a
20	POLR2A	chr8:11685644-11686591	K562	blood:	n/a	n/a
21	POLR2A	chr8:11685202-11686692	GM12891	blood:	n/a	n/a
22	POLR2A	chr8:11685760-11687288	K562	blood:	n/a	n/a
23	POLR2A	chr8:11685676-11686394	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr8:11685652-11686332	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11662802..11665653-chr8:11685244..11688002,2	K562	blood:

No data

Variant related genes	Relation type
FDFT1	TF binding region
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10095823	1.00[CHB][hapmap]
rs10098874	0.88[CEU][hapmap]
rs1047643	0.88[CEU][hapmap];1.00[CHD][hapmap]
rs1138666	1.00[ASN][1000 genomes]
rs12543666	1.00[ASN][1000 genomes]
rs12545992	1.00[CHB][hapmap]
rs17153710	1.00[CHB][hapmap]
rs2230070	1.00[CHD][hapmap]
rs2409836	1.00[CHD][hapmap]
rs3088244	0.92[CEU][hapmap]
rs34809309	1.00[ASN][1000 genomes]
rs4442098	1.00[ASN][1000 genomes]
rs4841600	1.00[CHD][hapmap]
rs4841604	1.00[CHD][hapmap]
rs57720356	1.00[ASN][1000 genomes]
rs57725348	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60856203	1.00[ASN][1000 genomes]
rs6601627	1.00[CHB][hapmap]
rs6601628	1.00[CHB][hapmap]
rs6601630	1.00[CHB][hapmap]
rs6983419	1.00[CHB][hapmap]
rs6994126	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6996029	1.00[CHB][hapmap]
rs6998854	1.00[CHB][hapmap]
rs7000179	1.00[CHB][hapmap]
rs7009163	0.94[CEU][hapmap]
rs7009514	0.82[CEU][hapmap]
rs73547796	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73549728	1.00[ASN][1000 genomes]
rs73549729	1.00[ASN][1000 genomes]
rs7818816	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7818952	1.00[ASN][1000 genomes]
rs8191595	1.00[CHB][hapmap]
rs8191649	1.00[CHD][hapmap]
rs9720275	1.00[CHB][hapmap]
rs9886596	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers 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	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1034132	chr8:11657033-12198242	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
15	nsv890365	chr8:11666451-11735641	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv890366	chr8:11666451-11900847	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	20 gene(s)	inside rSNPs	diseases
17	nsv1031158	chr8:11666558-11759064	Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv539477	chr8:11666558-11759064	Enhancers Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv1018042	chr8:11667496-11882385	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv890367	chr8:11668153-11793529	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv890368	chr8:11671041-11718528	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv890369	chr8:11671041-11840011	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
23	nsv1016952	chr8:11679271-11849955	Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
24	nsv1029093	chr8:11679271-11858466	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv539478	chr8:11679271-11858466	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10089520	PCDHGB4	trans	multi-tissue	Pritchard
rs10089520	CTSB	cis	multi-tissue	Pritchard
rs10089520	KLP1	trans	multi-tissue	Pritchard
rs10089520	P2RY6	trans	multi-tissue	Pritchard
rs10089520	ANTXR1	trans	multi-tissue	Pritchard
rs10089520	KCNJ8	trans	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11667000-11711000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:11669400-11708000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr8:11670000-11689200	Weak transcription	Fetal Heart	heart
4	chr8:11671400-11701400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:11675200-11707000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:11675800-11712600	Strong transcription	Dnd41	blood
7	chr8:11676000-11690600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:11676200-11704800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr8:11677000-11705200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:11677200-11690600	Strong transcription	HMEC	breast
11	chr8:11677200-11690800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr8:11677200-11704400	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr8:11677400-11690400	Strong transcription	NHEK	skin
14	chr8:11677600-11688600	Strong transcription	Fetal Intestine Small	intestine
15	chr8:11677600-11691800	Strong transcription	Osteobl	bone
16	chr8:11677600-11702000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr8:11677600-11702000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:11677600-11703200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr8:11677600-11708200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:11677600-11710600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:11677600-11711800	Strong transcription	Fetal Brain Female	brain
22	chr8:11677800-11690600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:11677800-11706600	Strong transcription	NHLF	lung
24	chr8:11678000-11693400	Strong transcription	A549	lung
25	chr8:11678000-11707400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr8:11678200-11691400	Strong transcription	Fetal Thymus	thymus
27	chr8:11678200-11697800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:11678200-11704000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:11678200-11704400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr8:11678200-11704600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr8:11678200-11705200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr8:11678200-11705200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr8:11678200-11706800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr8:11678400-11690400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr8:11678400-11692800	Strong transcription	Liver	Liver
36	chr8:11678400-11698000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr8:11678400-11704000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:11678400-11704400	Strong transcription	GM12878-XiMat	blood
39	chr8:11678400-11705600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr8:11678400-11706400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr8:11678600-11691600	Strong transcription	Placenta	Placenta
42	chr8:11678600-11693800	Weak transcription	Right Atrium	heart
43	chr8:11678600-11705400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr8:11678600-11708600	Strong transcription	HUVEC	blood vessel
45	chr8:11678800-11697800	Strong transcription	Lung	lung
46	chr8:11679000-11691400	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr8:11679000-11702200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr8:11679000-11705200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr8:11679000-11715200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:11679200-11689600	Strong transcription	Esophagus	oesophagus

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