Variant report

Variant	rs871694
Chromosome Location	chr4:55708824-55708825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr4:55708403-55708854	HL-60	blood:	n/a	chr4:55708622-55708629 chr4:55708620-55708633
2	HDAC2	chr4:55708365-55708947	MCF-7	breast:	n/a	n/a
3	NR2F2	chr4:55708307-55709011	MCF-7	breast:	n/a	n/a
4	ZNF217	chr4:55708298-55709045	MCF-7	breast:	n/a	n/a
5	NR2F2	chr4:55708430-55708984	MCF-7	breast:	n/a	n/a
6	GATA3	chr4:55708437-55708992	MCF-7	breast:	n/a	chr4:55708588-55708597
7	TAL1	chr4:55708734-55708981	K562	blood:	n/a	n/a
8	SIN3AK20	chr4:55708378-55709159	MCF-7	breast:	n/a	n/a
9	GATA3	chr4:55708268-55709130	MCF-7	breast:	n/a	chr4:55708588-55708597

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:55708795-55708845	AG10803	skin:	n/a
2	chr4:55708795-55708845	HAEpiC	amniotic membrane:	n/a
3	chr4:55708795-55708845	NT2-D1	testis:	n/a
4	chr4:55708795-55708845	LNCaP	prostate:	n/a
5	chr4:55708795-55708845	HRCEpiC	kidney:	n/a
6	chr4:55708795-55708845	HMEC	breast:	n/a
7	chr4:55708795-55708845	RPTEC	kidney:	n/a
8	chr4:55708795-55708845	HCPEpiC	choroid plexus:	n/a
9	chr4:55708795-55708845	AG09309	skin:	n/a
10	chr4:55708795-55708845	Caco-2	colon:	n/a
11	chr4:55708795-55708845	AG04449	skin:	fetal
12	chr4:55708795-55708845	SK-N-MC	brain:	n/a
13	chr4:55708795-55708845	NH-A	brain:	n/a
14	chr4:55708795-55708845	PFSK-1	brain:	n/a
15	chr4:55708795-55708845	SKMC	muscle:	n/a
16	chr4:55708795-55708845	SK-N-SH_RA	brain:	n/a
17	chr4:55708795-55708845	CMK	blood:	n/a
18	chr4:55708795-55708845	HCT-116	colon:	n/a
19	chr4:55708795-55708845	Hela-S3	cervix:	n/a
20	chr4:55708795-55708845	GM19239	blood:	n/a
21	chr4:55708795-55708845	T-47D	breast:	n/a
22	chr4:55708795-55708845	HRE	kidney:	n/a
23	chr4:55708795-55708845	HPAEpiC	pulmonary alveolar:	n/a
24	chr4:55708795-55708845	AoSMC	blood vessel:	n/a
25	chr4:55708795-55708845	BJ	skin:	n/a
26	chr4:55708795-55708845	IMR90	lung:	fetal
27	chr4:55708795-55708845	NHDF-neo	bronchial:	n/a
28	chr4:55708795-55708845	Hepatocyte	liver:	n/a
29	chr4:55708795-55708845	HCM	heart:	n/a
30	chr4:55708795-55708845	ProgFib	skin:	n/a
31	chr4:55708795-55708845	BE2_C	brain:	n/a
32	chr4:55708795-55708845	Jurkat	blood:	n/a
33	chr4:55708795-55708845	ovcar-3	ovarian:	n/a
34	chr4:55708795-55708845	SAEC	small airway:	n/a
35	chr4:55708795-55708845	HRPEpiC	eye:	n/a
36	chr4:55708795-55708845	ECC-1	luminal epithelium:	n/a
37	chr4:55708795-55708845	AG09319	gingival:	n/a
38	chr4:55708795-55708845	GM06990	blood:	n/a
39	chr4:55708795-55708845	AG04450	lung:	fetal
40	chr4:55708795-55708845	PANC-1	pancreas:	n/a
41	chr4:55708795-55708845	MCF10A-Er-Src	breast:	n/a
42	chr4:55708795-55708845	K562	blood:	n/a
43	chr4:55708795-55708845	HepG2	liver:	n/a
44	chr4:55708795-55708845	PrEC	prostate:	n/a
45	chr4:55708795-55708845	SK-N-SH	brain:	n/a
46	chr4:55708795-55708845	HIPEpiC	eye:	n/a
47	chr4:55708795-55708845	GM12892	blood:	n/a
48	chr4:55708795-55708845	A549	lung:	n/a
49	chr4:55708795-55708845	HNPCEpiC	eye:	n/a
50	chr4:55708795-55708845	U87	brain:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:55647754..55648646-chr4:55708231..55709242,4	MCF-7	breast:
2	chr4:55524498..55525559-chr4:55707619..55708970,5	MCF-7	breast:
3	chr4:55708158..55708934-chr4:55820918..55821668,3	MCF-7	breast:
4	chr4:55452869..55453638-chr4:55708509..55709111,2	MCF-7	breast:
5	chr4:55707866..55710526-chr4:55713081..55715385,2	MCF-7	breast:
6	chr4:55524498..55525559-chr4:55707838..55708970,3	MCF-7	breast:
7	chr4:55708346..55709146-chr4:55827430..55828429,3	MCF-7	breast:
8	chr4:55708184..55709079-chr4:55827341..55828314,6	MCF-7	breast:
9	chr4:55708286..55708872-chr4:55827341..55828280,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251256	TF binding region
ENSG00000251256	CpG island

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1123272	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1497476	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1497477	1.00[CEU][hapmap];0.96[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1497491	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1497492	0.88[ASN][1000 genomes]
rs17695485	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1948607	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055222	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132879	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2132880	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2173228	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2646314	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2646316	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2646317	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2646318	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2646319	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2646320	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2646351	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2646355	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2646364	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2646365	0.88[ASN][1000 genomes]
rs2646368	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2646369	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2726610	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2726612	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2726613	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2726619	0.91[ASN][1000 genomes]
rs2726620	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2726621	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2726623	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2726626	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2726627	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2726628	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2726629	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2726630	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2726631	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2726632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628137	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4280801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7662457	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7668976	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7686543	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7692346	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7697169	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs871692	0.93[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1836939	chr4:55701134-55716601	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55704600-55712600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:55705600-55711400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:55706600-55709000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr4:55706800-55709000	Enhancers	Primary hematopoietic stem cells	blood
5	chr4:55706800-55709800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:55707800-55709000	Enhancers	Placenta	Placenta
7	chr4:55707800-55709600	Enhancers	Left Ventricle	heart
8	chr4:55708400-55709000	Enhancers	Stomach Smooth Muscle	stomach
9	chr4:55708400-55709200	Enhancers	Fetal Stomach	stomach
10	chr4:55708400-55709600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:55708600-55709000	Enhancers	Fetal Lung	lung
12	chr4:55708800-55709000	Enhancers	Brain Hippocampus Middle	brain
13	chr4:55708800-55710000	Enhancers	Fetal Heart	heart

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