Variant report

Variant	rs1247299
Chromosome Location	chr6:161347496-161347497
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:1)
LncRNA
region (count:1)
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	chr6:161347487-161347537	NHBE	bronchial:	n/a
2	chr6:161347487-161347537	AoSMC	blood vessel:	n/a
3	chr6:161347487-161347537	HUVEC	blood vessel:	n/a
4	chr6:161347487-161347537	GM06990	blood:	n/a
5	chr6:161347487-161347537	NH-A	brain:	n/a
6	chr6:161347487-161347537	HCM	heart:	n/a
7	chr6:161347487-161347537	HNPCEpiC	eye:	n/a
8	chr6:161347487-161347537	MCF10A-Er-Src	breast:	n/a
9	chr6:161347487-161347537	HCPEpiC	choroid plexus:	n/a
10	chr6:161347487-161347537	H1-hESC	embryonic stem cell:	embryo
11	chr6:161347487-161347537	AG04449	skin:	fetal
12	chr6:161347487-161347537	BJ	skin:	n/a
13	chr6:161347487-161347537	HRE	kidney:	n/a
14	chr6:161347487-161347537	NB4	blood:	n/a
15	chr6:161347487-161347537	HRCEpiC	kidney:	n/a
16	chr6:161347487-161347537	CMK	blood:	n/a
17	chr6:161347487-161347537	HRPEpiC	eye:	n/a
18	chr6:161347487-161347537	NT2-D1	testis:	n/a
19	chr6:161347487-161347537	T-47D	breast:	n/a
20	chr6:161347487-161347537	ProgFib	skin:	n/a
21	chr6:161347487-161347537	AG09319	gingival:	n/a
22	chr6:161347487-161347537	AG10803	skin:	n/a
23	chr6:161347487-161347537	LNCaP	prostate:	n/a
24	chr6:161347487-161347537	NHDF-neo	bronchial:	n/a
25	chr6:161347487-161347537	SK-N-SH_RA	brain:	n/a
26	chr6:161347487-161347537	PANC-1	pancreas:	n/a
27	chr6:161347487-161347537	Hepatocyte	liver:	n/a
28	chr6:161347487-161347537	HepG2	liver:	n/a
29	chr6:161347487-161347537	SKMC	muscle:	n/a
30	chr6:161347487-161347537	AG09309	skin:	n/a
31	chr6:161347487-161347537	AG04450	lung:	fetal
32	chr6:161347487-161347537	HAEpiC	amniotic membrane:	n/a
33	chr6:161347487-161347537	IMR90	lung:	fetal
34	chr6:161347487-161347537	ovcar-3	ovarian:	n/a
35	chr6:161347487-161347537	HEEpiC	esophagus:	n/a
36	chr6:161347487-161347537	HEK293	kidney:	embryo
37	chr6:161347487-161347537	ECC-1	luminal epithelium:	n/a
38	chr6:161347487-161347537	Caco-2	colon:	n/a
39	chr6:161347487-161347537	A549	lung:	n/a
40	chr6:161347487-161347537	HIPEpiC	eye:	n/a
41	chr6:161347487-161347537	GM12891	blood:	n/a
42	chr6:161347487-161347537	SK-N-MC	brain:	n/a
43	chr6:161347487-161347537	K562	blood:	n/a
44	chr6:161347487-161347537	U87	brain:	n/a
45	chr6:161347487-161347537	GM19239	blood:	n/a
46	chr6:161347487-161347537	Jurkat	blood:	n/a
47	chr6:161347487-161347537	GM12878	blood:	n/a
48	chr6:161347487-161347537	RPTEC	kidney:	n/a
49	chr6:161347487-161347537	MCF-7	breast:	n/a
50	chr6:161347487-161347537	BE2_C	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161346875..161349133-chr6:161350824..161353127,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP3K4-2	chr6:161347401-161347610	ENSG00000233342

No data

Variant related genes	Relation type
ENSG00000231863	CpG island
ENSG00000231863	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11970528	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1247294	1.00[ASN][1000 genomes]
rs1247298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1247300	1.00[ASN][1000 genomes]
rs1247302	1.00[ASN][1000 genomes]
rs1247305	0.98[ASN][1000 genomes]
rs1247307	0.96[ASN][1000 genomes]
rs1247308	1.00[JPT][hapmap]
rs1247309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1247310	0.98[ASN][1000 genomes]
rs1247312	0.96[ASN][1000 genomes]
rs1247313	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1247316	0.98[ASN][1000 genomes]
rs1247317	0.98[ASN][1000 genomes]
rs1247318	0.98[ASN][1000 genomes]
rs1247319	0.98[ASN][1000 genomes]
rs1247320	0.98[ASN][1000 genomes]
rs1247321	0.98[ASN][1000 genomes]
rs1247322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1247323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1247325	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1247326	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1247327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1247328	0.89[ASN][1000 genomes]
rs1247329	0.88[ASN][1000 genomes]
rs1247330	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1247360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1247361	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1247362	1.00[ASN][1000 genomes]
rs1247363	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1247364	1.00[ASN][1000 genomes]
rs1247365	1.00[ASN][1000 genomes]
rs1663025	0.94[ASN][1000 genomes]
rs1937474	0.81[ASN][1000 genomes]
rs1937476	0.82[EUR][1000 genomes]
rs2465834	0.81[JPT][hapmap]
rs2465869	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2465870	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2465871	0.80[ASN][1000 genomes]
rs2465876	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2465877	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2465878	0.81[ASN][1000 genomes]
rs2489955	0.93[JPT][hapmap]
rs2489956	0.93[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs581947	0.92[ASN][1000 genomes]
rs585649	0.93[ASN][1000 genomes]
rs591676	0.92[ASN][1000 genomes]
rs62436898	0.94[ASN][1000 genomes]
rs638141	0.93[ASN][1000 genomes]
rs687701	0.93[ASN][1000 genomes]
rs935182	0.95[ASN][1000 genomes]
rs935183	0.98[ASN][1000 genomes]
rs9355851	0.82[ASN][1000 genomes]
rs9364580	0.87[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830853	chr6:161180005-161376481	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161334200-161347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161340000-161352000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:161341400-161350800	Weak transcription	GM12878-XiMat	blood
4	chr6:161343400-161351600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:161347200-161349200	Enhancers	Placenta	Placenta
6	chr6:161347400-161347600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:161347400-161347600	Enhancers	Esophagus	oesophagus

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