Variant report

Variant	rs1024598
Chromosome Location	chr17:67175668-67175669
allele	C/T
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	EBF1	chr17:67175354-67175728	GM12878	blood:	n/a	chr17:67175550-67175561
2	GATA3	chr17:67175629-67176252	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr17:67175531-67175731	MCF10A-Er-Src	breast:	n/a	n/a
4	EBF1	chr17:67175342-67176121	GM12878	blood:	n/a	chr17:67175550-67175561
5	POLR2A	chr17:67175617-67175698	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr17:67175559-67176092	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ABCA10	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1011789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11077396	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11077403	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11077408	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11077414	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11077942	0.84[TSI][hapmap]
rs1118164	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654430	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11655199	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658738	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659091	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs11659119	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11868299	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12451663	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12940557	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12941264	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12943387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948396	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12950143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12951091	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12952984	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12953127	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs1558167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1974575	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs1974578	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2215149	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302132	0.84[TSI][hapmap]
rs2302133	0.84[TSI][hapmap]
rs2302134	0.84[TSI][hapmap]
rs2364990	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364991	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364992	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4358004	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968841	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968842	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968843	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs4968849	0.84[GIH][hapmap]
rs4968850	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968851	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs5025273	0.81[CHB][hapmap]
rs62082734	0.85[ASN][1000 genomes]
rs7208382	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7212188	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7217887	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs721813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7221183	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7223736	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs740517	0.84[TSI][hapmap]
rs740520	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs7504026	0.88[CHB][hapmap];0.91[CHD][hapmap]
rs8064583	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8065924	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066449	0.87[GIH][hapmap]
rs8066629	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8067584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8069791	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8070459	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8071249	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071373	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8071611	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8073982	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8074654	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs8075377	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8077551	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs8079681	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080065	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080693	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8080863	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs9709278	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs981452	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs981453	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9894644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9902643	0.87[GIH][hapmap];0.80[TSI][hapmap]
rs9909216	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9910035	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9912127	0.87[GIH][hapmap];0.80[TSI][hapmap]

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	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	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
4	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457888	chr17:67149973-67226643	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv575931	chr17:67149973-67226643	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv575933	chr17:67153386-67215712	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1024598	ABCA8	cis	cerebellum	SCAN
rs1024598	ABCA6	cis	parietal	SCAN
rs1024598	CACNG5	cis	cerebellum	SCAN
rs1024598	ABCA6	cis	cerebellum	SCAN
rs1024598	ABCA8	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67138800-67182000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:67144000-67175800	Weak transcription	Gastric	stomach
3	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
4	chr17:67148800-67190200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr17:67150800-67192400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr17:67150800-67193200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr17:67151600-67178000	Weak transcription	Liver	Liver
8	chr17:67160600-67220000	Weak transcription	Fetal Lung	lung
9	chr17:67163400-67181200	Weak transcription	Left Ventricle	heart
10	chr17:67172200-67182800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr17:67172400-67191400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr17:67172800-67178000	Weak transcription	Adipose Nuclei	Adipose
13	chr17:67173200-67193000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr17:67173400-67230000	Weak transcription	Pancreas	Pancrea
15	chr17:67174200-67175800	Strong transcription	Ovary	ovary
16	chr17:67174200-67176000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:67174200-67176000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:67174200-67176000	Enhancers	HMEC	breast
19	chr17:67174200-67176200	Enhancers	Hela-S3	cervix
20	chr17:67174200-67176200	Enhancers	NHEK	skin
21	chr17:67174400-67176000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:67174600-67176800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:67175200-67176200	Enhancers	Fetal Intestine Small	intestine
24	chr17:67175200-67176600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr17:67175200-67176600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:67175400-67175800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr17:67175400-67176000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr17:67175400-67176000	Enhancers	K562	blood
29	chr17:67175400-67176000	Enhancers	NHDF-Ad	bronchial
30	chr17:67175400-67176200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:67175400-67176200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr17:67175400-67176200	Enhancers	Stomach Mucosa	stomach
33	chr17:67175400-67176400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:67175400-67176400	Enhancers	Osteobl	bone
35	chr17:67175400-67176600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:67175400-67176600	Enhancers	Primary hematopoietic stem cells	blood
37	chr17:67175600-67175800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:67175600-67175800	Enhancers	A549	lung
39	chr17:67175600-67176000	Enhancers	Primary B cells from peripheral blood	blood
40	chr17:67175600-67176000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr17:67175600-67176000	Enhancers	Fetal Intestine Large	intestine
42	chr17:67175600-67176000	Enhancers	GM12878-XiMat	blood
43	chr17:67175600-67176000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr17:67175600-67176400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr17:67175600-67176600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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