Variant report

Variant	rs11613495
Chromosome Location	chr12:4554630-4554631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:4554623-4554673	ovcar-3	ovarian:	n/a
2	chr12:4554623-4554673	HepG2	liver:	n/a
3	chr12:4554596-4554646	HNPCEpiC	eye:	n/a
4	chr12:4554596-4554646	HRPEpiC	eye:	n/a
5	chr12:4554623-4554673	GM12891	blood:	n/a
6	chr12:4554596-4554646	PFSK-1	brain:	n/a
7	chr12:4554596-4554646	HEK293	kidney:	embryo
8	chr12:4554596-4554646	A549	lung:	n/a
9	chr12:4554623-4554673	GM06990	blood:	n/a
10	chr12:4554623-4554673	LNCaP	prostate:	n/a
11	chr12:4554623-4554673	H1-hESC	embryonic stem cell:	embryo
12	chr12:4554623-4554673	PFSK-1	brain:	n/a
13	chr12:4554596-4554646	HRE	kidney:	n/a
14	chr12:4554623-4554673	PANC-1	pancreas:	n/a
15	chr12:4554596-4554646	NHDF-neo	bronchial:	n/a
16	chr12:4554623-4554673	HUVEC	blood vessel:	n/a
17	chr12:4554596-4554646	ProgFib	skin:	n/a
18	chr12:4554596-4554646	HCF	heart:	n/a
19	chr12:4554623-4554673	A549	lung:	n/a
20	chr12:4554596-4554646	HepG2	liver:	n/a
21	chr12:4554623-4554673	AG10803	skin:	n/a
22	chr12:4554596-4554646	RPTEC	kidney:	n/a
23	chr12:4554596-4554646	GM06990	blood:	n/a
24	chr12:4554623-4554673	U87	brain:	n/a
25	chr12:4554596-4554646	HMEC	breast:	n/a
26	chr12:4554596-4554646	IMR90	lung:	fetal
27	chr12:4554596-4554646	HL-60	blood:	n/a
28	chr12:4554596-4554646	HIPEpiC	eye:	n/a
29	chr12:4554596-4554646	LNCaP	prostate:	n/a
30	chr12:4554596-4554646	HRCEpiC	kidney:	n/a
31	chr12:4554596-4554646	NT2-D1	testis:	n/a
32	chr12:4554596-4554646	AG09309	skin:	n/a
33	chr12:4554596-4554646	HCT-116	colon:	n/a
34	chr12:4554623-4554673	NHBE	bronchial:	n/a
35	chr12:4554623-4554673	HRE	kidney:	n/a
36	chr12:4554596-4554646	HUVEC	blood vessel:	n/a
37	chr12:4554623-4554673	HCPEpiC	choroid plexus:	n/a
38	chr12:4554623-4554673	GM12892	blood:	n/a
39	chr12:4554596-4554646	SKMC	muscle:	n/a
40	chr12:4554596-4554646	MCF-7	breast:	n/a
41	chr12:4554623-4554673	HEEpiC	esophagus:	n/a
42	chr12:4554623-4554673	HRCEpiC	kidney:	n/a
43	chr12:4554623-4554673	HCM	heart:	n/a
44	chr12:4554596-4554646	NH-A	brain:	n/a
45	chr12:4554596-4554646	SAEC	small airway:	n/a
46	chr12:4554623-4554673	Hepatocyte	liver:	n/a
47	chr12:4554596-4554646	PrEC	prostate:	n/a
48	chr12:4554623-4554673	NB4	blood:	n/a
49	chr12:4554596-4554646	SK-N-SH_RA	brain:	n/a
50	chr12:4554596-4554646	K562	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4550824..4553664-chr12:4554520..4557456,3	K562	blood:

No data

Variant related genes	Relation type
FGF6	CpG island
ENSG00000111241	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10744641	1.00[JPT][hapmap]
rs10849038	1.00[JPT][hapmap]
rs11063099	1.00[JPT][hapmap]
rs11063156	1.00[JPT][hapmap]
rs11610220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11610225	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11611403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177165	1.00[ASN][1000 genomes]
rs17177242	1.00[ASN][1000 genomes]
rs17183633	1.00[ASN][1000 genomes]
rs2970822	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2970823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2970828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2970829	1.00[ASN][1000 genomes]
rs2970830	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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898616	chr12:4490059-4564613	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585	chr12:4514249-4559242	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv33276	chr12:4553216-4554993	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11613495	ENO2	cis	cerebellum	SCAN
rs11613495	LRTM2	cis	cerebellum	SCAN
rs11613495	FBXL14	cis	cerebellum	SCAN
rs11613495	TULP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4548600-4554800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr12:4549600-4558800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:4551000-4559000	Weak transcription	Right Atrium	heart
4	chr12:4551600-4556400	Weak transcription	Fetal Brain Male	brain
5	chr12:4551800-4556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:4551800-4559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:4552000-4558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:4552600-4554800	Active TSS	Fetal Muscle Leg	muscle
9	chr12:4553400-4559000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:4553600-4559000	Weak transcription	Fetal Thymus	thymus
11	chr12:4553800-4558200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:4553800-4559000	Weak transcription	Dnd41	blood
13	chr12:4554000-4555000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr12:4554000-4555800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr12:4554200-4554800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:4554200-4554800	Enhancers	Psoas Muscle	Psoas
17	chr12:4554200-4555200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:4554400-4555000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr12:4554400-4555400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:4554400-4558200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:4554600-4554800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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