Variant report

Variant	rs9828976
Chromosome Location	chr3:136536835-136536836
allele	C/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	MXI1	chr3:136536205-136539806	SK-N-SH	brain:	n/a	n/a
2	ZMIZ1	chr3:136536708-136538142	K562	blood:	n/a	n/a
3	CTCF	chr3:136536444-136538013	A549	lung:	n/a	n/a
4	SMARCC1	chr3:136536631-136539432	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr3:136536662-136539311	Hela-S3	cervix:	n/a	n/a
6	ZKSCAN1	chr3:136536730-136538878	Hela-S3	cervix:	n/a	n/a
7	RFX5	chr3:136536804-136539811	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:136468701..136475672-chr3:136535815..136540749,9	K562	blood:
2	chr3:136535239..136537634-chr3:136579848..136582645,2	MCF-7	breast:
3	chr3:136536665..136539935-chr3:136579370..136582081,3	K562	blood:

Variant related genes	Relation type
SLC35G2	TF binding region
ENSG00000158092	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1052620	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062352	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	1.00[ASN][1000 genomes]
rs13080786	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100192	1.00[ASN][1000 genomes]
rs13314357	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433683	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	1.00[ASN][1000 genomes]
rs13434116	1.00[ASN][1000 genomes]
rs17365792	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872239	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176269	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370972	1.00[ASN][1000 genomes]
rs28390205	1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28489326	1.00[ASN][1000 genomes]
rs28641809	1.00[ASN][1000 genomes]
rs28750366	1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34564818	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34804893	1.00[ASN][1000 genomes]
rs35096613	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100027	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35198484	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35210994	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35422852	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35428413	1.00[ASN][1000 genomes]
rs35880395	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36109616	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36177165	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4038586	1.00[ASN][1000 genomes]
rs4470449	1.00[ASN][1000 genomes]
rs66509730	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	1.00[ASN][1000 genomes]
rs6767889	1.00[ASN][1000 genomes]
rs6806123	1.00[ASN][1000 genomes]
rs71336069	1.00[ASN][1000 genomes]
rs71336080	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs73230099	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231903	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289513	0.83[EUR][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813376	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819856	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820717	1.00[ASN][1000 genomes]
rs9838884	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840500	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845862	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847427	1.00[ASN][1000 genomes]
rs9850364	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857833	1.00[ASN][1000 genomes]
rs9858560	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865995	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867325	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871184	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873536	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875770	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879531	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881831	1.00[ASN][1000 genomes]
rs9883189	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136535400-136537200	Enhancers	Fetal Lung	lung
2	chr3:136535600-136537200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr3:136535800-136537000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:136535800-136537200	Enhancers	Brain Anterior Caudate	brain
5	chr3:136535800-136537200	Enhancers	Brain Germinal Matrix	brain
6	chr3:136536000-136537000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:136536000-136537000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:136536000-136537200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:136536000-136537200	Enhancers	A549	lung
10	chr3:136536000-136537400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:136536200-136537000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:136536200-136537200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:136536200-136537200	Enhancers	Brain Hippocampus Middle	brain
14	chr3:136536400-136537000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:136536400-136537000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:136536400-136537000	Enhancers	Dnd41	blood
17	chr3:136536400-136537400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:136536600-136537000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
19	chr3:136536600-136537000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr3:136536600-136537000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:136536600-136537000	Enhancers	Hela-S3	cervix
22	chr3:136536600-136537200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:136536600-136537200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:136536600-136537200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:136536600-136537200	Enhancers	Adipose Nuclei	Adipose
26	chr3:136536600-136537200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:136536600-136537200	Enhancers	HUVEC	blood vessel
28	chr3:136536600-136537200	Enhancers	NHLF	lung
29	chr3:136536600-136537200	Enhancers	Osteobl	bone
30	chr3:136536600-136537400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:136536800-136537000	Active TSS	Primary T cells from cord blood	blood
32	chr3:136536800-136537000	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:136536800-136537000	Enhancers	Fetal Stomach	stomach
34	chr3:136536800-136537000	Flanking Active TSS	HepG2	liver
35	chr3:136536800-136537000	Enhancers	NH-A	brain
36	chr3:136536800-136537200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:136536800-136537200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:136536800-136537200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:136536800-136537200	Enhancers	Brain Substantia Nigra	brain
40	chr3:136536800-136539600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:136536800-136539600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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