Variant report

Variant	rs1980307
Chromosome Location	chr7:99060603-99060604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99060265-99060669	K562	blood:	n/a	n/a
2	POLR2A	chr7:99060489-99060671	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:99060528-99060682	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:99059955-99061034	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:99060355-99060744	K562	blood:	n/a	n/a
6	POLR2A	chr7:99060421-99060675	K562	blood:	n/a	n/a
7	POLR2A	chr7:99060254-99060743	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr7:99060259-99061405	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99060187..99063147-chr7:99085147..99088743,3	K562	blood:
2	chr7:99058626..99061250-chr7:99076948..99079594,2	K562	blood:
3	chr7:99055792..99058380-chr7:99059202..99061148,2	MCF-7	breast:
4	chr20:45958949..45961670-chr7:99060355..99062544,2	MCF-7	breast:
5	chr7:99059967..99062594-chr7:99515447..99517524,2	K562	blood:
6	chr7:99060444..99064436-chr7:99153650..99156512,4	K562	blood:
7	chr7:99055033..99067556-chr7:99095016..99105645,21	K562	blood:
8	chr7:99007269..99009205-chr7:99058762..99060773,2	MCF-7	breast:

No data

Variant related genes	Relation type
ATP5J2	TF binding region
ENSG00000106245	Chromatin interaction
ENSG00000196652	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000197343	Chromatin interaction
ENSG00000272647	Chromatin interaction
ENSG00000146833	Chromatin interaction
ENSG00000241468	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011024	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10155966	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10225314	0.87[JPT][hapmap]
rs10238965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10243678	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10244158	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253937	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10254729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs10270459	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs10270917	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs10271049	1.00[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];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271582	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10272998	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap]
rs10279308	0.84[CEU][hapmap]
rs1043466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464604	0.81[ASN][1000 genomes]
rs11539770	0.81[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs11772470	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11976018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11978089	0.84[CEU][hapmap]
rs12538826	0.82[ASN][1000 genomes]
rs13227795	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240600	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437771	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003499	0.84[CEU][hapmap]
rs2072181	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2240384	1.00[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];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240385	0.85[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2272168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280600	0.91[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];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286162	0.92[CEU][hapmap]
rs2404324	0.93[EUR][1000 genomes]
rs28457808	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28495024	0.81[AMR][1000 genomes]
rs3137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34777615	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3779354	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3800960	0.85[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs3801288	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs3843540	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901286	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45492098	0.81[ASN][1000 genomes]
rs45540134	0.87[ASN][1000 genomes]
rs45622743	0.83[ASN][1000 genomes]
rs4729532	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs58222677	0.84[ASN][1000 genomes]
rs61159815	0.85[ASN][1000 genomes]
rs61402640	0.81[ASN][1000 genomes]
rs61543997	0.81[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs6955490	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs6961634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6962772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794682	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804551	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868564	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs883403	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917154	1.00[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];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs940336	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1980307	ACTL6B	cis	cerebellum	SCAN
rs1980307	GATS	cis	parietal	SCAN
rs1980307	CYP3A5	cis	parietal	SCAN
rs1980307	CPSF4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99038000-99061600	Strong transcription	Fetal Stomach	stomach
2	chr7:99038200-99061800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr7:99038200-99061800	Strong transcription	Fetal Intestine Small	intestine
4	chr7:99038200-99062000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:99038200-99062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:99038200-99062400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:99038400-99062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:99038600-99062400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:99039200-99061600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:99039600-99062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:99040400-99060800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr7:99040400-99062000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr7:99040800-99062000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr7:99046600-99062800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:99056400-99061600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr7:99057000-99062400	Weak transcription	Fetal Kidney	kidney
17	chr7:99057000-99062800	Weak transcription	HSMMtube	muscle
18	chr7:99057200-99062400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:99057200-99062600	Weak transcription	Stomach Mucosa	stomach
20	chr7:99057400-99061800	Genic enhancers	HepG2	liver
21	chr7:99057400-99063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:99057600-99062600	Weak transcription	Small Intestine	intestine
23	chr7:99057800-99061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:99058000-99061400	Weak transcription	NHDF-Ad	bronchial
25	chr7:99058000-99061600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:99058000-99062200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:99058000-99062600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:99058200-99061400	Genic enhancers	K562	blood
29	chr7:99058200-99062000	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr7:99058400-99061400	Weak transcription	Brain Germinal Matrix	brain
31	chr7:99058400-99061600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:99058400-99061600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:99058400-99061800	Weak transcription	Brain Anterior Caudate	brain
34	chr7:99058400-99062400	Weak transcription	Colonic Mucosa	Colon
35	chr7:99058400-99062600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:99058400-99063000	Weak transcription	Ovary	ovary
37	chr7:99058600-99061400	Weak transcription	NHLF	lung
38	chr7:99058600-99062600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:99058800-99061200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:99058800-99061800	Weak transcription	Fetal Heart	heart
41	chr7:99058800-99062400	Weak transcription	Right Atrium	heart
42	chr7:99059000-99061800	Weak transcription	Brain Angular Gyrus	brain
43	chr7:99059000-99062000	Strong transcription	Fetal Thymus	thymus
44	chr7:99059000-99062600	Weak transcription	Fetal Brain Female	brain
45	chr7:99059000-99062800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:99059000-99063000	Weak transcription	Aorta	Aorta
47	chr7:99059400-99061000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:99059400-99061200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:99059400-99061600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:99059400-99061600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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