Variant report

Variant	rs360097
Chromosome Location	chr1:226065755-226065756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:226065316-226065788	MCF-7	breast:	n/a	n/a
2	RAD21	chr1:226065292-226065867	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:226065373-226065755	K562	blood:	n/a	n/a
4	ZNF263	chr1:226065084-226065816	HEK293-T-REx	kidney:	n/a	n/a
5	CTCF	chr1:226065209-226065964	A549	lung:	n/a	n/a
6	RAD21	chr1:226065354-226065825	A549	lung:	n/a	n/a
7	CTCF	chr1:226065001-226065946	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr1:226065292-226065870	K562	blood:	n/a	n/a
9	CTCF	chr1:226065620-226065770	HAc	cerebellar:	n/a	n/a
10	CTCF	chr1:226065381-226065756	GM12878	blood:	n/a	n/a
11	RAD21	chr1:226065311-226065856	MCF-7	breast:	n/a	n/a
12	RAD21	chr1:226065232-226065823	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 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	chr1:226053163..226055606-chr1:226064903..226066639,3	K562	blood:
4	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
5	chr1:226033230..226036408-chr1:226061975..226066194,3	MCF-7	breast:
6	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:
7	chr1:226065700..226068385-chr1:226110654..226114654,4	K562	blood:

No data

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000154380	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000143819	Chromatin interaction
ENSG00000242861	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs111990	0.86[AFR][1000 genomes]
rs1223244	0.82[EUR][1000 genomes]
rs12747508	0.81[EUR][1000 genomes]
rs168617	0.82[EUR][1000 genomes]
rs168618	0.85[AFR][1000 genomes]
rs168619	0.85[AFR][1000 genomes]
rs2292563	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292564	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2740168	0.85[JPT][hapmap]
rs360060	0.86[EUR][1000 genomes]
rs360076	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes]
rs360088	0.83[AFR][1000 genomes]
rs360091	0.87[AFR][1000 genomes]
rs360093	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360094	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360095	0.91[AFR][1000 genomes]
rs360096	0.91[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360098	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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs360100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360101	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360102	0.88[ASW][hapmap];0.91[CEU][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs360103	1.00[ASW][hapmap];0.83[CEU][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs3820236	0.95[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs55936398	0.92[ASN][1000 genomes]
rs6426090	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515156	0.82[EUR][1000 genomes]
rs9919303	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[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	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
rs360097	TMEM63A	cis	cerebellum	SCAN
rs360097	TMEM63A	cis	parietal	SCAN
rs360097	PARP1	cis	cerebellum	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	chr1:226036800-226066600	Weak transcription	Fetal Brain Male	brain
3	chr1:226038800-226065800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:226044600-226065800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:226050200-226068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:226051800-226066400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr1:226054400-226065800	Weak transcription	HUVEC	blood vessel
8	chr1:226054600-226065800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:226054800-226065800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:226055000-226066600	Weak transcription	Dnd41	blood
11	chr1:226058400-226067200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:226059600-226068800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:226059800-226066600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:226059800-226066800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:226060200-226068600	Weak transcription	NH-A	brain
16	chr1:226060600-226066400	Genic enhancers	Placenta	Placenta
17	chr1:226060800-226066000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:226062000-226067200	Genic enhancers	Fetal Intestine Large	intestine
19	chr1:226062200-226065800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:226062800-226066400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:226062800-226066600	Genic enhancers	Fetal Thymus	thymus
22	chr1:226062800-226067000	Genic enhancers	Fetal Intestine Small	intestine
23	chr1:226063000-226066400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:226063000-226066600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:226063000-226068200	Genic enhancers	Fetal Muscle Leg	muscle
26	chr1:226063200-226068200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:226063400-226067800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:226063600-226067000	Enhancers	Colonic Mucosa	Colon
29	chr1:226064000-226065800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:226064200-226066600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:226064200-226068000	Weak transcription	NHEK	skin
32	chr1:226064400-226067800	Weak transcription	HMEC	breast
33	chr1:226064600-226065800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:226064600-226067200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:226064600-226067200	Enhancers	Fetal Heart	heart
36	chr1:226064600-226067400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:226064800-226065800	Genic enhancers	Colon Smooth Muscle	Colon
38	chr1:226064800-226066000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:226064800-226066000	Enhancers	HSMMtube	muscle
40	chr1:226064800-226066800	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr1:226064800-226067200	Genic enhancers	NHLF	lung
42	chr1:226064800-226067600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:226064800-226068200	Enhancers	NHDF-Ad	bronchial
44	chr1:226065000-226065800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:226065000-226065800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:226065000-226065800	Genic enhancers	Primary T cells from cord blood	blood
47	chr1:226065000-226065800	Genic enhancers	Lung	lung
48	chr1:226065000-226066000	Enhancers	HSMM	muscle
49	chr1:226065000-226066200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:226065000-226066400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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