Variant report

Variant	rs8077252
Chromosome Location	chr17:67085062-67085063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr17:67084984-67085129	K562	blood:	n/a	n/a
2	TEAD4	chr17:67084710-67085192	K562	blood:	n/a	n/a
3	ZNF143	chr17:67085001-67085352	K562	blood:	n/a	n/a
4	TEAD4	chr17:67084770-67085132	K562	blood:	n/a	n/a
5	TRIM28	chr17:67084825-67085305	K562	blood:	n/a	n/a
6	KAP1	chr17:67084776-67085691	K562	blood:	n/a	n/a
7	EP300	chr17:67084782-67085225	K562	blood:	n/a	n/a
8	RCOR1	chr17:67084731-67085242	K562	blood:	n/a	n/a
9	RCOR1	chr17:67084862-67085115	K562	blood:	n/a	n/a
10	ZMIZ1	chr17:67084942-67085122	K562	blood:	n/a	n/a
11	NR2F2	chr17:67084722-67085209	K562	blood:	n/a	n/a
12	CBX3	chr17:67084746-67085330	K562	blood:	n/a	n/a
13	TAL1	chr17:67084744-67085162	K562	blood:	n/a	n/a
14	GATA2	chr17:67084781-67085128	K562	blood:	n/a	n/a
15	TBL1XR1	chr17:67084794-67085355	K562	blood:	n/a	n/a
16	JUND	chr17:67084801-67085101	K562	blood:	n/a	n/a
17	CEBPD	chr17:67084722-67085160	K562	blood:	n/a	n/a
18	BHLHE40	chr17:67084981-67085086	K562	blood:	n/a	n/a
19	CBX3	chr17:67084988-67085319	K562	blood:	n/a	n/a
20	NR2F2	chr17:67084608-67085274	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	chr17:67084611..67087550-chr17:67148578..67150089,2	K562	blood:

No data

Variant related genes	Relation type
ABCA6	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11077942	0.82[TSI][hapmap]
rs11652530	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12162136	0.86[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453914	0.86[CHB][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs12601388	0.82[EUR][1000 genomes]
rs12939282	0.84[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12940298	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12952117	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs12953127	0.86[TSI][hapmap]
rs16973567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041170	0.84[EUR][1000 genomes]
rs2041171	0.86[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2190900	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2302132	0.82[TSI][hapmap]
rs2302133	0.82[TSI][hapmap]
rs2302134	0.85[JPT][hapmap];0.82[TSI][hapmap]
rs3744489	0.86[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4141177	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4334355	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4603621	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4968838	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4968839	0.87[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4968843	1.00[ASW][hapmap];0.86[TSI][hapmap]
rs4968849	0.81[TSI][hapmap]
rs4968851	0.86[TSI][hapmap]
rs5025273	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6501183	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7207609	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7208586	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7213831	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7214079	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7217887	0.86[ASW][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap]
rs740516	0.82[JPT][hapmap]
rs740517	0.82[TSI][hapmap]
rs740520	0.86[TSI][hapmap]
rs7503217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8064595	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8066449	0.85[TSI][hapmap]
rs8074654	0.86[TSI][hapmap]
rs8077551	0.86[TSI][hapmap]
rs8078314	0.84[EUR][1000 genomes]
rs8079981	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8080863	0.86[TSI][hapmap]
rs9303012	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs976698	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs981452	0.86[TSI][hapmap]
rs9902643	1.00[ASW][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap]
rs9912127	0.86[TSI][hapmap]
rs9916693	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs997781	0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1066998	chr17:67060038-67090475	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv908705	chr17:67061898-67112456	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	esv1850212	chr17:67081732-67117428	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8077252	ABCA9	cis	parietal	SCAN
rs8077252	ABCA6	cis	parietal	SCAN
rs8077252	ABCA6	cis	cerebellum	SCAN
rs8077252	CACNG5	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67065600-67088600	Weak transcription	Pancreas	Pancrea
2	chr17:67067200-67099600	Weak transcription	Gastric	stomach
3	chr17:67067200-67111600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr17:67071800-67091400	Weak transcription	Brain Anterior Caudate	brain
5	chr17:67075600-67085600	Strong transcription	Fetal Lung	lung
6	chr17:67076800-67109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr17:67079400-67087400	Weak transcription	Colon Smooth Muscle	Colon
9	chr17:67079400-67090600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:67079400-67093600	Weak transcription	Fetal Stomach	stomach
11	chr17:67079400-67095600	Weak transcription	Psoas Muscle	Psoas
12	chr17:67079400-67112200	Strong transcription	Liver	Liver
13	chr17:67079400-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:67079400-67117600	Weak transcription	Esophagus	oesophagus
15	chr17:67079600-67091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr17:67079600-67101200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:67079600-67114200	Weak transcription	NHDF-Ad	bronchial
18	chr17:67080600-67086600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:67080800-67088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:67080800-67088600	Weak transcription	GM12878-XiMat	blood
21	chr17:67080800-67090800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:67080800-67112000	Weak transcription	Brain Substantia Nigra	brain
23	chr17:67081200-67086200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:67081200-67088200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:67081200-67088600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:67081200-67090800	Weak transcription	Fetal Muscle Leg	muscle
27	chr17:67081200-67102000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr17:67081400-67089400	Weak transcription	Ovary	ovary
29	chr17:67081400-67090400	Weak transcription	Left Ventricle	heart
30	chr17:67081400-67095000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:67081400-67118600	Weak transcription	Right Ventricle	heart
32	chr17:67082200-67114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:67083800-67090200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr17:67084200-67089000	Weak transcription	Adipose Nuclei	Adipose
35	chr17:67085000-67086600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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