Variant report

Variant	rs12233696
Chromosome Location	chr4:90759637-90759638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr4:90757293-90759857	H1-neurons	neurons:	n/a	chr4:90758798-90758811 chr4:90758722-90758742 chr4:90758722-90758742 chr4:90757347-90757360 chr4:90758747-90758760 chr4:90758202-90758215
2	MXI1	chr4:90757102-90760194	SK-N-SH	brain:	n/a	n/a
3	TAL1	chr4:90759433-90759661	K562	blood:	n/a	n/a
4	RFX5	chr4:90757013-90759936	SK-N-SH	brain:	n/a	n/a
5	GATA1	chr4:90758615-90760183	PBDE	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MMRN1-1	chr4:90759412-90761746	ENSG00000247775

Variant related genes	Relation type
SNCA	TF binding region

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

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

rs_ID	r²[population]
rs10516846	0.81[AFR][1000 genomes]
rs10516847	1.00[CEU][hapmap]
rs12643790	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1372512	0.84[EUR][1000 genomes]
rs1442132	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17016196	0.81[AFR][1000 genomes]
rs17016274	0.96[ASN][1000 genomes]
rs2870027	0.92[AFR][1000 genomes]
rs3729594	1.00[CEU][hapmap]
rs3775435	1.00[CEU][hapmap]
rs3775438	1.00[CEU][hapmap]
rs3775442	1.00[CEU][hapmap]
rs3775444	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs3775450	1.00[CEU][hapmap];0.82[AFR][1000 genomes]
rs3796667	0.85[AFR][1000 genomes]
rs3822091	1.00[CEU][hapmap]
rs3898322	1.00[CEU][hapmap]
rs58108801	0.94[ASN][1000 genomes]
rs58165695	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60341854	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532200	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6816633	0.96[ASN][1000 genomes]
rs6825073	0.81[AFR][1000 genomes]
rs7657014	0.81[ASN][1000 genomes]
rs7699596	0.81[AFR][1000 genomes]
rs961386	1.00[CEU][hapmap];0.81[AFR][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	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS 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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90755600-90759800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:90756800-90759800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:90757200-90759800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90757400-90760200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:90757800-90759800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:90758000-90759800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:90758200-90759800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:90758600-90759800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr4:90758800-90759800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:90758800-90760000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:90759000-90760000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:90759000-90760000	Flanking Active TSS	Dnd41	blood
13	chr4:90759400-90759800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr4:90759400-90759800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:90759400-90759800	Bivalent/Poised TSS	Fetal Lung	lung
16	chr4:90759400-90759800	Active TSS	HMEC	breast
17	chr4:90759600-90759800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:90759600-90759800	Enhancers	Fetal Brain Female	brain
19	chr4:90759600-90759800	Flanking Active TSS	HUVEC	blood vessel
20	chr4:90759600-90760000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:90759600-90760000	Enhancers	Primary T cells from cord blood	blood
22	chr4:90759600-90760000	Enhancers	Primary hematopoietic stem cells	blood
23	chr4:90759600-90760000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:90759600-90771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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