Variant report

Variant	rs12197340
Chromosome Location	chr6:49467096-49467097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:49466882-49467181	T-47D	breast:	n/a	n/a
2	GATA3	chr6:49466900-49467187	T-47D	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:49467064-49467114	U87	brain:	n/a
2	chr6:49467064-49467114	NT2-D1	testis:	n/a
3	chr6:49467064-49467114	HCM	heart:	n/a
4	chr6:49467064-49467114	GM12878	blood:	n/a
5	chr6:49467064-49467114	AG09309	skin:	n/a
6	chr6:49467064-49467114	HIPEpiC	eye:	n/a
7	chr6:49467064-49467114	NHBE	bronchial:	n/a
8	chr6:49467064-49467114	PANC-1	pancreas:	n/a
9	chr6:49467064-49467114	ovcar-3	ovarian:	n/a
10	chr6:49467064-49467114	AG04450	lung:	fetal
11	chr6:49467064-49467114	NHDF-neo	bronchial:	n/a
12	chr6:49467064-49467114	NB4	blood:	n/a
13	chr6:49467064-49467114	Hepatocyte	liver:	n/a
14	chr6:49467064-49467114	HRPEpiC	eye:	n/a
15	chr6:49467064-49467114	HepG2	liver:	n/a
16	chr6:49467064-49467114	Jurkat	blood:	n/a
17	chr6:49467064-49467114	H1-hESC	embryonic stem cell:	embryo
18	chr6:49467064-49467114	MCF-7	breast:	n/a
19	chr6:49467064-49467114	AG04449	skin:	fetal
20	chr6:49467064-49467114	GM12891	blood:	n/a
21	chr6:49467064-49467114	HCT-116	colon:	n/a
22	chr6:49467064-49467114	LNCaP	prostate:	n/a
23	chr6:49467064-49467114	SK-N-MC	brain:	n/a
24	chr6:49467064-49467114	GM12892	blood:	n/a
25	chr6:49467064-49467114	HPAEpiC	pulmonary alveolar:	n/a
26	chr6:49467064-49467114	SK-N-SH_RA	brain:	n/a
27	chr6:49467064-49467114	AG10803	skin:	n/a
28	chr6:49467064-49467114	Caco-2	colon:	n/a
29	chr6:49467064-49467114	SK-N-SH	brain:	n/a
30	chr6:49467064-49467114	HEEpiC	esophagus:	n/a
31	chr6:49467064-49467114	HEK293	kidney:	embryo
32	chr6:49467064-49467114	HCF	heart:	n/a
33	chr6:49467064-49467114	MCF10A-Er-Src	breast:	n/a
34	chr6:49467064-49467114	AoSMC	blood vessel:	n/a
35	chr6:49467064-49467114	NH-A	brain:	n/a
36	chr6:49467064-49467114	BJ	skin:	n/a
37	chr6:49467064-49467114	GM06990	blood:	n/a
38	chr6:49467064-49467114	SKMC	muscle:	n/a
39	chr6:49467064-49467114	K562	blood:	n/a
40	chr6:49467064-49467114	BE2_C	brain:	n/a
41	chr6:49467064-49467114	Hela-S3	cervix:	n/a
42	chr6:49467064-49467114	ECC-1	luminal epithelium:	n/a
43	chr6:49467064-49467114	PFSK-1	brain:	n/a
44	chr6:49467064-49467114	SAEC	small airway:	n/a
45	chr6:49467064-49467114	AG09319	gingival:	n/a
46	chr6:49467064-49467114	RPTEC	kidney:	n/a
47	chr6:49467064-49467114	ProgFib	skin:	n/a
48	chr6:49467064-49467114	HUVEC	blood vessel:	n/a
49	chr6:49467064-49467114	HCPEpiC	choroid plexus:	n/a
50	chr6:49467064-49467114	HNPCEpiC	eye:	n/a

No data

Variant related genes	Relation type
GLYATL3	TF binding region
GLYATL3	CpG island

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10948505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189789	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190697	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12191171	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202875	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204398	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204617	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206768	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208117	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208221	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214010	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214609	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17663557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17663627	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127756	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127759	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229385	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57912929	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6928563	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774623	0.86[EUR][1000 genomes];0.90[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS 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	19 gene(s)	inside rSNPs	diseases
3	nsv1019611	chr6:49431569-49470663	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49432600-49472000	Weak transcription	NHEK	skin
2	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:49458400-49472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:49458600-49473800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:49460400-49473200	Weak transcription	HepG2	liver
6	chr6:49460600-49473600	Weak transcription	Stomach Mucosa	stomach
7	chr6:49461400-49472400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:49466800-49467600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:49467000-49467200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:49467000-49467200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:49467000-49467200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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