Variant report

Variant	rs360098
Chromosome Location	chr1:226066690-226066691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226066537-226066747	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:226066684-226066690	K562	blood:	n/a	n/a
3	CEBPB	chr1:226066608-226066804	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:226063406..226070293-chr1:226107715..226112317,7	K562	blood:
2	chr1:225997762..225999546-chr1:226064729..226066981,2	MCF-7	breast:
3	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
4	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:
5	chr1:226066286..226068064-chr1:226160996..226163119,2	K562	blood:
6	chr1:226066024..226068193-chr1:226076140..226078255,2	MCF-7	breast:
7	chr1:226065700..226068385-chr1:226110654..226114654,4	K562	blood:
8	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000143819	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1223244	0.82[AMR][1000 genomes]
rs12747508	0.98[ASN][1000 genomes]
rs168617	0.84[AMR][1000 genomes]
rs2292563	0.91[CEU][hapmap]
rs2292564	0.91[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs360060	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs360076	0.91[CEU][hapmap]
rs360093	0.95[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs360094	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs360096	0.91[CEU][hapmap]
rs360097	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs360099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360100	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs360101	0.91[CEU][hapmap]
rs360102	0.91[CEU][hapmap]
rs360103	0.83[CEU][hapmap]
rs360104	0.91[CHB][hapmap]
rs3820236	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515156	0.98[ASN][1000 genomes]
rs9919303	0.82[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap]

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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs360098	PARP1	cis	cerebellum	SCAN
rs360098	TMEM63A	cis	cerebellum	SCAN
rs360098	TMEM63A	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr1:226050200-226068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:226058400-226067200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:226059600-226068800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:226059800-226066800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
6	chr1:226060200-226068600	Weak transcription	NH-A	brain
7	chr1:226062000-226067200	Genic enhancers	Fetal Intestine Large	intestine
8	chr1:226062800-226067000	Genic enhancers	Fetal Intestine Small	intestine
9	chr1:226063000-226068200	Genic enhancers	Fetal Muscle Leg	muscle
10	chr1:226063200-226068200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:226063400-226067800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:226063600-226067000	Enhancers	Colonic Mucosa	Colon
13	chr1:226064200-226068000	Weak transcription	NHEK	skin
14	chr1:226064400-226067800	Weak transcription	HMEC	breast
15	chr1:226064600-226067200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:226064600-226067200	Enhancers	Fetal Heart	heart
17	chr1:226064600-226067400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:226064800-226066800	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr1:226064800-226067200	Genic enhancers	NHLF	lung
20	chr1:226064800-226067600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:226064800-226068200	Enhancers	NHDF-Ad	bronchial
22	chr1:226065000-226066800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:226065000-226067000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:226065000-226067200	Genic enhancers	Gastric	stomach
25	chr1:226065000-226068000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:226065000-226068800	Enhancers	Left Ventricle	heart
27	chr1:226065000-226068800	Enhancers	Psoas Muscle	Psoas
28	chr1:226065000-226068800	Enhancers	Right Ventricle	heart
29	chr1:226065000-226068800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:226065000-226069200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:226065200-226067400	Enhancers	Liver	Liver
32	chr1:226065200-226068200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:226065200-226068600	Enhancers	Aorta	Aorta
34	chr1:226065200-226068800	Enhancers	Right Atrium	heart
35	chr1:226065200-226069000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:226065400-226066800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:226065400-226066800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:226065400-226066800	Enhancers	A549	lung
39	chr1:226065400-226068000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:226065400-226068000	Enhancers	Stomach Mucosa	stomach
41	chr1:226065400-226068200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:226065400-226068400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
43	chr1:226065400-226068600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:226065400-226069000	Enhancers	Brain Angular Gyrus	brain
45	chr1:226065400-226069400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr1:226065600-226066800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:226065600-226066800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:226065600-226066800	Enhancers	Osteobl	bone
49	chr1:226065600-226067000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:226065600-226067000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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