Variant report

Variant	rs13240600
Chromosome Location	chr7:99064466-99064467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr7:99063068-99064606	K562	blood:	n/a	n/a
2	POLR2A	chr7:99064447-99064466	Hela-S3	cervix:	n/a	n/a
3	ZNF384	chr7:99063634-99064500	K562	blood:	n/a	n/a
4	YY1	chr7:99063258-99064543	SK-N-SH	brain:	n/a	chr7:99063756-99063768 chr7:99063540-99063554
5	RCOR1	chr7:99064454-99064520	HepG2	liver:	n/a	n/a
6	HCFC1	chr7:99062769-99064523	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr7:99062753-99064532	SK-N-SH	brain:	n/a	n/a
8	GTF3C2	chr7:99063746-99064519	K562	blood:	n/a	n/a
9	ESRRA	chr7:99062811-99064524	GM12878	blood:	n/a	chr7:99063418-99063431
10	POLR2A	chr7:99062009-99064593	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99062243..99066385-chr7:99154728..99156714,5	K562	blood:
2	chr7:99061566..99064955-chr7:99096123..99100968,5	MCF-7	breast:
3	chr7:99062320..99065185-chr7:99213079..99214681,2	K562	blood:
4	chr7:99062287..99065237-chr7:99068917..99072408,9	MCF-7	breast:
5	chr7:98987157..98988975-chr7:99062223..99064769,2	MCF-7	breast:
6	chr7:99061682..99064704-chr7:99696557..99699487,3	K562	blood:
7	chr7:99004357..99008691-chr7:99061400..99066308,7	K562	blood:
8	chr7:99004357..99007369-chr7:99061400..99065046,4	K562	blood:
9	chr7:99062251..99065366-chr7:99100921..99104362,4	MCF-7	breast:
10	chr7:99055033..99067556-chr7:99095016..99105645,21	K562	blood:
11	chr7:99063380..99066123-chr7:99095103..99099037,3	MCF-7	breast:
12	chr7:99035887..99038153-chr7:99062281..99064908,3	MCF-7	breast:

No data

Variant related genes	Relation type
PTCD1	TF binding region
ATP5J2-PTCD1	TF binding region
ATP5J2	TF binding region
ENSG00000106245	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000197037	Chromatin interaction
ENSG00000198556	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000196652	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000197343	Chromatin interaction
ENSG00000272647	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000166508	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011024	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10155966	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs10215854	0.81[CEU][hapmap]
rs10225314	0.93[JPT][hapmap]
rs10238965	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10243678	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs10244158	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253937	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10254729	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10258757	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs10270459	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs10270917	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs10271049	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271582	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10272998	0.82[CEU][hapmap]
rs10273424	0.89[CEU][hapmap]
rs1043466	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464604	0.81[ASN][1000 genomes]
rs10808112	0.81[CEU][hapmap]
rs11539770	0.81[ASN][1000 genomes]
rs11762273	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs11772470	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs11973173	0.81[CEU][hapmap]
rs11976018	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12538826	0.82[ASN][1000 genomes]
rs13227795	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437771	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161698	0.83[JPT][hapmap]
rs1980307	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]
rs2072181	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs2240384	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240385	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2269985	0.83[JPT][hapmap]
rs2272168	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280600	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]
rs2280601	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286162	0.83[CEU][hapmap]
rs2404324	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28457808	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28495024	0.80[AMR][1000 genomes]
rs3137	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34257469	0.81[CEU][hapmap]
rs34777615	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764815	0.83[JPT][hapmap]
rs3779354	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3800960	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3801288	0.82[CEU][hapmap]
rs3843540	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901286	0.89[AMR][1000 genomes];0.86[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]
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	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs6961634	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6962772	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794682	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794705	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804551	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868564	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs883403	0.92[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917154	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs940336	0.91[CHB][hapmap];0.94[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

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99063400-99064600	Active TSS	Hela-S3	cervix
2	chr7:99063800-99064600	Active TSS	HepG2	liver
3	chr7:99063800-99067800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:99064200-99064600	Enhancers	Primary B cells from peripheral blood	blood
5	chr7:99064200-99065600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:99064200-99065600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:99064200-99066800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:99064200-99066800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:99064200-99066800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:99064200-99067000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:99064200-99067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:99064200-99067000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr7:99064200-99067000	Weak transcription	NHEK	skin
14	chr7:99064200-99067000	Weak transcription	Osteobl	bone
15	chr7:99064200-99067200	Weak transcription	Right Atrium	heart
16	chr7:99064200-99067600	Weak transcription	Pancreas	Pancrea
17	chr7:99064200-99068000	Weak transcription	Spleen	Spleen
18	chr7:99064200-99068000	Weak transcription	K562	blood
19	chr7:99064200-99068800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:99064200-99068800	Weak transcription	Brain Angular Gyrus	brain
21	chr7:99064200-99068800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:99064200-99069000	Weak transcription	Lung	lung
23	chr7:99064200-99069600	Weak transcription	Esophagus	oesophagus
24	chr7:99064200-99069800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:99064200-99069800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:99064200-99069800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:99064200-99070000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:99064200-99070000	Weak transcription	Gastric	stomach
29	chr7:99064400-99064600	Enhancers	Dnd41	blood
30	chr7:99064400-99066400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:99064400-99066800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr7:99064400-99066800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr7:99064400-99066800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:99064400-99066800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:99064400-99067000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:99064400-99067000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:99064400-99067200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:99064400-99067200	Weak transcription	Adipose Nuclei	Adipose
39	chr7:99064400-99067400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr7:99064400-99067400	Weak transcription	Psoas Muscle	Psoas
41	chr7:99064400-99068000	Weak transcription	Placenta	Placenta
42	chr7:99064400-99068800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:99064400-99068800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:99064400-99068800	Weak transcription	Liver	Liver
45	chr7:99064400-99068800	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:99064400-99068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:99064400-99069000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr7:99064400-99069000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:99064400-99069000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:99064400-99069000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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