Variant report

Variant	rs2397153
Chromosome Location	chr6:53882366-53882367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:53882326-53882376	MCF10A-Er-Src	breast:	n/a
2	chr6:53882326-53882376	T-47D	breast:	n/a
3	chr6:53882326-53882376	HCT-116	colon:	n/a
4	chr6:53882326-53882376	HepG2	liver:	n/a
5	chr6:53882326-53882376	NB4	blood:	n/a
6	chr6:53882326-53882376	HCF	heart:	n/a
7	chr6:53882326-53882376	SK-N-SH_RA	brain:	n/a
8	chr6:53882326-53882376	AG10803	skin:	n/a
9	chr6:53882326-53882376	AG04450	lung:	fetal
10	chr6:53882326-53882376	Hepatocyte	liver:	n/a
11	chr6:53882326-53882376	AoSMC	blood vessel:	n/a
12	chr6:53882326-53882376	SKMC	muscle:	n/a
13	chr6:53882326-53882376	Jurkat	blood:	n/a
14	chr6:53882326-53882376	GM19239	blood:	n/a
15	chr6:53882326-53882376	BJ	skin:	n/a
16	chr6:53882326-53882376	GM06990	blood:	n/a
17	chr6:53882326-53882376	NHDF-neo	bronchial:	n/a
18	chr6:53882326-53882376	HAEpiC	amniotic membrane:	n/a
19	chr6:53882326-53882376	ECC-1	luminal epithelium:	n/a
20	chr6:53882326-53882376	GM12891	blood:	n/a
21	chr6:53882326-53882376	Hela-S3	cervix:	n/a
22	chr6:53882326-53882376	HRPEpiC	eye:	n/a
23	chr6:53882326-53882376	NH-A	brain:	n/a
24	chr6:53882326-53882376	AG09309	skin:	n/a
25	chr6:53882326-53882376	Caco-2	colon:	n/a
26	chr6:53882326-53882376	ProgFib	skin:	n/a
27	chr6:53882326-53882376	GM12892	blood:	n/a
28	chr6:53882326-53882376	U87	brain:	n/a
29	chr6:53882326-53882376	AG09319	gingival:	n/a
30	chr6:53882326-53882376	HMEC	breast:	n/a
31	chr6:53882326-53882376	SAEC	small airway:	n/a
32	chr6:53882326-53882376	MCF-7	breast:	n/a
33	chr6:53882326-53882376	RPTEC	kidney:	n/a
34	chr6:53882326-53882376	BE2_C	brain:	n/a
35	chr6:53882326-53882376	IMR90	lung:	fetal
36	chr6:53882326-53882376	CMK	blood:	n/a
37	chr6:53882326-53882376	PrEC	prostate:	n/a
38	chr6:53882326-53882376	HCM	heart:	n/a
39	chr6:53882326-53882376	GM12878	blood:	n/a
40	chr6:53882326-53882376	LNCaP	prostate:	n/a
41	chr6:53882326-53882376	H1-hESC	embryonic stem cell:	embryo
42	chr6:53882326-53882376	HRCEpiC	kidney:	n/a
43	chr6:53882326-53882376	HNPCEpiC	eye:	n/a
44	chr6:53882326-53882376	HCPEpiC	choroid plexus:	n/a
45	chr6:53882326-53882376	HEEpiC	esophagus:	n/a
46	chr6:53882326-53882376	ovcar-3	ovarian:	n/a
47	chr6:53882326-53882376	HRE	kidney:	n/a
48	chr6:53882326-53882376	PFSK-1	brain:	n/a
49	chr6:53882326-53882376	SK-N-MC	brain:	n/a
50	chr6:53882326-53882376	SK-N-SH	brain:	n/a

No data

Variant related genes	Relation type
ERHP2	CpG island
MLIP	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1022929	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1022930	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1022931	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10484651	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10484652	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10484653	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10948794	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948795	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1156379	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs1156380	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs11961988	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194304	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12195852	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12199925	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12201302	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12524379	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12529752	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1325821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1409101	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570911	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1570912	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16884583	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4712052	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4715435	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62397360	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6914051	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6929778	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9349692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9357783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9370254	0.87[ASN][1000 genomes]
rs9370255	0.85[ASN][1000 genomes]
rs9370256	0.85[ASN][1000 genomes]
rs9382274	0.95[ASN][1000 genomes]
rs9395900	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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53875600-53883600	Weak transcription	Left Ventricle	heart
2	chr6:53876400-53883400	Weak transcription	Right Atrium	heart
3	chr6:53878200-53882600	Weak transcription	Liver	Liver
4	chr6:53879600-53883400	Weak transcription	Psoas Muscle	Psoas
5	chr6:53880200-53883200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:53880400-53882400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:53881200-53883400	Weak transcription	Fetal Intestine Small	intestine
8	chr6:53881400-53883000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:53881400-53883400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:53881600-53883600	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:53882200-53883000	Enhancers	HSMMtube	muscle
12	chr6:53882200-53883200	Enhancers	Fetal Heart	heart
13	chr6:53882200-53884000	Enhancers	HSMM	muscle
14	chr6:53882200-53887400	Active TSS	Skeletal Muscle Female	skeletal muscle

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