Variant report

Variant	rs330920
Chromosome Location	chr8:8997614-8997615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr8:8997404-8997982	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr8:8997376-8997882	SK-N-MC	brain:	n/a	n/a
3	MYC	chr8:8997612-8997982	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr8:8997466-8999259	K562	blood:	n/a	n/a
5	POLR2A	chr8:8997397-8998017	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr8:8997512-8998030	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr8:8997381-8998190	HUVEC	blood vessel:	n/a	n/a
8	FOS	chr8:8997468-8997965	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr8:8991597-8999830	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr8:8997364-8998081	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr8:8997288-8998045	HUVEC	blood vessel:	n/a	n/a
12	FOXP2	chr8:8997402-8998208	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr8:8997444-8997825	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000254340	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs12785	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs189798	0.80[EUR][1000 genomes]
rs330903	0.86[EUR][1000 genomes]
rs330904	0.87[EUR][1000 genomes]
rs330905	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs330908	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330909	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs330910	0.87[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs330911	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330912	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs330913	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs330914	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs330915	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330916	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330917	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330918	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs330919	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs330921	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs330922	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs330923	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs330924	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs408773	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9949	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active 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	22 gene(s)	inside rSNPs	diseases
7	nsv1026279	chr8:8982622-9030279	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS 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 miRNA target site	16 gene(s)	inside rSNPs	n/a
8	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs330920	DEFB136	cis	parietal	SCAN
rs330920	PPP1R3B	cis	lymphoblastoid	seeQTL
rs330920	C8orf79	cis	parietal	SCAN
rs330920	RP1L1	cis	cerebellum	SCAN
rs330920	DEFB134	cis	cerebellum	SCAN
rs330920	CTSB	cis	cerebellum	SCAN
rs330920	FLJ10661	cis	cerebellum	SCAN
rs330920	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8992600-9000000	Weak transcription	Hela-S3	cervix
2	chr8:8993400-8997800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:8993600-9005400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr8:8993800-8998400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:8993800-8998600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:8993800-9007400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:8994000-8997800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr8:8994000-8997800	Weak transcription	Brain Hippocampus Middle	brain
9	chr8:8994200-8997800	Weak transcription	A549	lung
10	chr8:8994200-9000800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr8:8994200-9005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr8:8994200-9007200	Weak transcription	Brain Angular Gyrus	brain
13	chr8:8994200-9007200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:8994200-9007200	Weak transcription	Fetal Brain Male	brain
15	chr8:8994400-8997800	Weak transcription	NHEK	skin
16	chr8:8994400-8998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:8994400-9001000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr8:8994400-9005200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr8:8994400-9005200	Weak transcription	Small Intestine	intestine
20	chr8:8994600-8997800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr8:8994600-8999600	Genic enhancers	HUVEC	blood vessel
22	chr8:8994600-9000400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:8994800-8998200	Genic enhancers	Fetal Intestine Large	intestine
24	chr8:8994800-8998600	Genic enhancers	Fetal Intestine Small	intestine
25	chr8:8994800-8999800	Strong transcription	Fetal Stomach	stomach
26	chr8:8994800-8999800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr8:8994800-9000000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:8994800-9000600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr8:8994800-9001000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:8994800-9001000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr8:8994800-9001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr8:8995000-8999200	Strong transcription	NHDF-Ad	bronchial
33	chr8:8995000-8999400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr8:8995000-9000600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr8:8995000-9000800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr8:8995200-8999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr8:8995200-8999800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr8:8995200-9000800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr8:8995200-9000800	Strong transcription	Fetal Muscle Leg	muscle
40	chr8:8995200-9004800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:8995400-8997800	Strong transcription	Placenta	Placenta
42	chr8:8995400-8997800	Weak transcription	Right Atrium	heart
43	chr8:8995400-8998400	Weak transcription	Stomach Mucosa	stomach
44	chr8:8995400-8999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr8:8995400-9000600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr8:8995400-9001000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr8:8995600-8998400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr8:8995600-9000600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:8995800-8998800	Genic enhancers	Fetal Heart	heart
50	chr8:8996200-8999200	Strong transcription	Muscle Satellite Cultured Cells	--

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