Variant report

Variant	rs6747466
Chromosome Location	chr2:55390814-55390815
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55384078..55385579-chr2:55388774..55390849,2	MCF-7	breast:
2	chr2:55279956..55282350-chr2:55389384..55392221,3	K562	blood:
3	chr2:55131884..55132585-chr2:55390651..55391252,2	MCF-7	breast:
4	chr2:55275064..55280479-chr2:55390367..55395295,9	MCF-7	breast:
5	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
6	chr2:55334946..55336599-chr2:55390126..55391859,2	MCF-7	breast:
7	chr2:55389326..55391363-chr2:55393207..55395340,2	K562	blood:
8	chr2:55273759..55277470-chr2:55389795..55392112,3	K562	blood:
9	chr2:55274543..55277923-chr2:55387934..55394752,12	MCF-7	breast:
10	chr2:55359631..55362469-chr2:55389581..55391287,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000266376	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10496038	1.00[CEU][hapmap]
rs1134722	0.86[EUR][1000 genomes]
rs11686766	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11686912	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11687876	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12989854	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12995548	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13000786	0.86[EUR][1000 genomes]
rs13003020	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13012567	0.86[EUR][1000 genomes]
rs13014752	0.92[EUR][1000 genomes]
rs13017468	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs13032294	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028139	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs34447956	0.86[EUR][1000 genomes]
rs35141050	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35183885	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs35227659	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35700883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36121000	0.86[EUR][1000 genomes]
rs4318424	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4627623	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6730950	0.84[JPT][hapmap]
rs6742306	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6743339	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71414544	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414546	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414547	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414548	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414549	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71414556	0.92[EUR][1000 genomes]
rs71414557	0.86[EUR][1000 genomes]
rs7595814	0.88[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55381000-55391000	Enhancers	Stomach Mucosa	stomach
2	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
3	chr2:55384000-55392800	Weak transcription	HMEC	breast
4	chr2:55384800-55392200	Weak transcription	Right Ventricle	heart
5	chr2:55386000-55395000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
7	chr2:55387400-55393800	Weak transcription	Fetal Heart	heart
8	chr2:55387400-55395600	Enhancers	Lung	lung
9	chr2:55387600-55395000	Weak transcription	Psoas Muscle	Psoas
10	chr2:55387800-55391000	Enhancers	Spleen	Spleen
11	chr2:55387800-55392400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:55388000-55391200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:55388000-55395200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:55388400-55392000	Enhancers	Fetal Brain Male	brain
15	chr2:55388400-55392200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:55388600-55391000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr2:55388600-55391200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:55388600-55392000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:55388600-55392400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55388600-55393200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:55388600-55393400	Enhancers	NH-A	brain
22	chr2:55388800-55391000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:55388800-55391600	Enhancers	Fetal Brain Female	brain
24	chr2:55388800-55391600	Enhancers	Gastric	stomach
25	chr2:55388800-55392200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:55388800-55392400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:55388800-55395000	Weak transcription	Left Ventricle	heart
28	chr2:55389000-55394800	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:55389000-55394800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:55389200-55391200	Enhancers	Adipose Nuclei	Adipose
31	chr2:55389200-55393200	Enhancers	HUVEC	blood vessel
32	chr2:55389200-55394000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:55389200-55394800	Enhancers	Brain Anterior Caudate	brain
34	chr2:55389200-55397400	Enhancers	NHLF	lung
35	chr2:55389400-55391600	Enhancers	HSMM	muscle
36	chr2:55389400-55394800	Enhancers	Brain Hippocampus Middle	brain
37	chr2:55389400-55395200	Weak transcription	NHEK	skin
38	chr2:55389600-55391200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:55389600-55392000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr2:55389600-55392400	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr2:55389800-55391200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:55389800-55391600	Enhancers	Placenta	Placenta
43	chr2:55389800-55392000	Enhancers	Fetal Lung	lung
44	chr2:55389800-55394000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:55389800-55394600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:55389800-55395000	Weak transcription	Brain Germinal Matrix	brain
47	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
48	chr2:55390000-55391400	Enhancers	Rectal Smooth Muscle	rectum
49	chr2:55390000-55391400	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:55390000-55393000	Enhancers	Colon Smooth Muscle	Colon

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