Variant report

Variant	rs13197588
Chromosome Location	chr6:49517758-49517759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:49517755-49519554	HCT-116	colon:	n/a	chr6:49518356-49518363
2	MAX	chr6:49517644-49519344	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
3	POLR2A	chr6:49517756-49519681	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:49517617-49517861	H1-hESC	embryonic stem cell:	n/a	n/a
5	HA-E2F1	chr6:49517738-49519388	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:49517402-49517882	MCF-7	breast:	n/a	n/a
7	E2F6	chr6:49517622-49519321	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr6:49517624-49519414	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
9	ZNF143	chr6:49517701-49519549	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr6:49517734-49519487	H1-hESC	embryonic stem cell:	n/a	chr6:49518356-49518363
11	TCF12	chr6:49517641-49518011	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:49517634-49519474	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr6:49517510-49519567	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:49517623-49519307	MCF-7	breast:	n/a	n/a
15	SP1	chr6:49517701-49518487	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr6:49517711-49519429	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:49517622-49519547	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:49517717-49518014	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3AK20	chr6:49517749-49519895	MCF-7	breast:	n/a	n/a
20	TBP	chr6:49517734-49519568	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr6:49517700-49518102	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:49517734-49517784	PANC-1	pancreas:	n/a
2	chr6:49517734-49517784	GM12878	blood:	n/a
3	chr6:49517734-49517784	HepG2	liver:	n/a
4	chr6:49517734-49517784	HRCEpiC	kidney:	n/a
5	chr6:49517734-49517784	ovcar-3	ovarian:	n/a
6	chr6:49517734-49517784	HPAEpiC	pulmonary alveolar:	n/a
7	chr6:49517734-49517784	NH-A	brain:	n/a
8	chr6:49517734-49517784	LNCaP	prostate:	n/a
9	chr6:49517734-49517784	Hela-S3	cervix:	n/a
10	chr6:49517734-49517784	Caco-2	colon:	n/a
11	chr6:49517734-49517784	HCT-116	colon:	n/a
12	chr6:49517734-49517784	SKMC	muscle:	n/a
13	chr6:49517734-49517784	U87	brain:	n/a
14	chr6:49517734-49517784	GM19239	blood:	n/a
15	chr6:49517734-49517784	HEK293	kidney:	embryo
16	chr6:49517734-49517784	SK-N-MC	brain:	n/a
17	chr6:49517734-49517784	BE2_C	brain:	n/a
18	chr6:49517734-49517784	NHDF-neo	bronchial:	n/a
19	chr6:49517734-49517784	MCF-7	breast:	n/a
20	chr6:49517734-49517784	SK-N-SH	brain:	n/a
21	chr6:49517734-49517784	AG09309	skin:	n/a
22	chr6:49517734-49517784	ProgFib	skin:	n/a
23	chr6:49517734-49517784	SAEC	small airway:	n/a
24	chr6:49517734-49517784	NHBE	bronchial:	n/a
25	chr6:49517734-49517784	BJ	skin:	n/a
26	chr6:49517734-49517784	GM12891	blood:	n/a
27	chr6:49517734-49517784	HL-60	blood:	n/a
28	chr6:49517734-49517784	HRPEpiC	eye:	n/a
29	chr6:49517734-49517784	HCM	heart:	n/a
30	chr6:49517734-49517784	AG09319	gingival:	n/a
31	chr6:49517734-49517784	HUVEC	blood vessel:	n/a
32	chr6:49517734-49517784	HNPCEpiC	eye:	n/a
33	chr6:49517734-49517784	AG10803	skin:	n/a
34	chr6:49517734-49517784	AG04450	lung:	fetal
35	chr6:49517734-49517784	HMEC	breast:	n/a
36	chr6:49517734-49517784	NT2-D1	testis:	n/a
37	chr6:49517734-49517784	Hepatocyte	liver:	n/a
38	chr6:49517734-49517784	PFSK-1	brain:	n/a
39	chr6:49517734-49517784	K562	blood:	n/a
40	chr6:49517734-49517784	GM06990	blood:	n/a
41	chr6:49517734-49517784	HCF	heart:	n/a
42	chr6:49517734-49517784	HRE	kidney:	n/a
43	chr6:49517734-49517784	GM12892	blood:	n/a
44	chr6:49517734-49517784	IMR90	lung:	fetal
45	chr6:49517734-49517784	HCPEpiC	choroid plexus:	n/a
46	chr6:49517734-49517784	Jurkat	blood:	n/a
47	chr6:49517734-49517784	T-47D	breast:	n/a
48	chr6:49517734-49517784	NB4	blood:	n/a
49	chr6:49517734-49517784	HAEpiC	amniotic membrane:	n/a
50	chr6:49517734-49517784	RPTEC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49515017..49518306-chr6:49519777..49524035,4	K562	blood:
2	chr6:49429390..49432411-chr6:49516710..49519961,3	MCF-7	breast:

No data

Variant related genes	Relation type
C6orf141	TF binding region
C6orf141	CpG island
ENSG00000197261	Chromatin interaction
ENSG00000031691	Chromatin interaction
ENSG00000146085	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12214715	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13196352	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13206340	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2127758	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715135	0.90[ASN][1000 genomes]
rs4715136	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749515	0.80[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.94[ASN][1000 genomes]
rs9463500	0.94[ASN][1000 genomes]
rs9463501	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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
5	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13197588	IL17A	cis	parietal	SCAN
rs13197588	C6orf141	cis	cerebellum	SCAN
rs13197588	MUT	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49510800-49517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:49516600-49517800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:49517200-49517800	Weak transcription	A549	lung
4	chr6:49517400-49517800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:49517400-49518000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:49517400-49519800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:49517400-49520000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:49517400-49520000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:49517600-49517800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:49517600-49517800	Enhancers	HMEC	breast
11	chr6:49517600-49517800	Enhancers	NHEK	skin
12	chr6:49517600-49518000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:49517600-49518000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:49517600-49518000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:49517600-49519800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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