Variant report

Variant	rs575885
Chromosome Location	chr6:163475289-163475290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:163475280-163475430	GM12867	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:163475252-163475302	NHDF-neo	bronchial:	n/a
2	chr6:163475252-163475302	PrEC	prostate:	n/a
3	chr6:163475252-163475302	HAEpiC	amniotic membrane:	n/a
4	chr6:163475252-163475302	K562	blood:	n/a
5	chr6:163475252-163475302	PANC-1	pancreas:	n/a
6	chr6:163475252-163475302	Jurkat	blood:	n/a
7	chr6:163475252-163475302	GM19239	blood:	n/a
8	chr6:163475252-163475302	H1-hESC	embryonic stem cell:	embryo
9	chr6:163475252-163475302	CMK	blood:	n/a
10	chr6:163475252-163475302	SK-N-SH_RA	brain:	n/a
11	chr6:163475252-163475302	HPAEpiC	pulmonary alveolar:	n/a
12	chr6:163475252-163475302	Caco-2	colon:	n/a
13	chr6:163475252-163475302	PFSK-1	brain:	n/a
14	chr6:163475252-163475302	HEEpiC	esophagus:	n/a
15	chr6:163475252-163475302	AG04450	lung:	fetal
16	chr6:163475252-163475302	BJ	skin:	n/a
17	chr6:163475252-163475302	ProgFib	skin:	n/a
18	chr6:163475252-163475302	NH-A	brain:	n/a
19	chr6:163475252-163475302	U87	brain:	n/a
20	chr6:163475252-163475302	HL-60	blood:	n/a
21	chr6:163475252-163475302	ECC-1	luminal epithelium:	n/a
22	chr6:163475252-163475302	RPTEC	kidney:	n/a
23	chr6:163475252-163475302	GM06990	blood:	n/a
24	chr6:163475252-163475302	HRPEpiC	eye:	n/a
25	chr6:163475252-163475302	HCT-116	colon:	n/a
26	chr6:163475252-163475302	HCPEpiC	choroid plexus:	n/a
27	chr6:163475252-163475302	HRCEpiC	kidney:	n/a
28	chr6:163475252-163475302	BE2_C	brain:	n/a
29	chr6:163475252-163475302	IMR90	lung:	fetal
30	chr6:163475252-163475302	ovcar-3	ovarian:	n/a
31	chr6:163475252-163475302	GM12892	blood:	n/a
32	chr6:163475252-163475302	HMEC	breast:	n/a
33	chr6:163475252-163475302	GM12878	blood:	n/a
34	chr6:163475252-163475302	HCM	heart:	n/a
35	chr6:163475252-163475302	HCF	heart:	n/a
36	chr6:163475252-163475302	HUVEC	blood vessel:	n/a
37	chr6:163475252-163475302	T-47D	breast:	n/a
38	chr6:163475252-163475302	SKMC	muscle:	n/a
39	chr6:163475252-163475302	HIPEpiC	eye:	n/a
40	chr6:163475252-163475302	AG10803	skin:	n/a
41	chr6:163475252-163475302	SAEC	small airway:	n/a
42	chr6:163475252-163475302	LNCaP	prostate:	n/a
43	chr6:163475252-163475302	HNPCEpiC	eye:	n/a
44	chr6:163475252-163475302	A549	lung:	n/a
45	chr6:163475252-163475302	Hepatocyte	liver:	n/a
46	chr6:163475252-163475302	HepG2	liver:	n/a
47	chr6:163475252-163475302	AoSMC	blood vessel:	n/a
48	chr6:163475252-163475302	AG04449	skin:	fetal
49	chr6:163475252-163475302	MCF10A-Er-Src	breast:	n/a
50	chr6:163475252-163475302	NHBE	bronchial:	n/a

No data

Variant related genes	Relation type
ENSG00000225437	TF binding region
ENSG00000225437	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2031436	0.86[AMR][1000 genomes]
rs2764003	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs491862	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528170	0.85[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs536655	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs547661	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs547694	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs568041	0.94[ASN][1000 genomes]
rs571644	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576854	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs580843	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6936045	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917926	chr6:162646457-163609259	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv605159	chr6:162800156-163479507	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv529089	chr6:163129464-163516451	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1026490	chr6:163133433-163705708	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv869286	chr6:163146342-163697445	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1030116	chr6:163273707-163525678	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1020900	chr6:163302262-163517812	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv916587	chr6:163337791-163606120	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1021433	chr6:163375760-163509866	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv605187	chr6:163448750-163496289	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1034556	chr6:163449712-163488528	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv538525	chr6:163449712-163488528	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163472200-163475800	Weak transcription	Pancreas	Pancrea
2	chr6:163474600-163475800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:163474800-163475600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:163475200-163475400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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