Variant report

Variant	rs6759911
Chromosome Location	chr2:55393962-55393963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55291031..55292984-chr2:55393872..55396324,2	K562	blood:
2	chr2:55389326..55391363-chr2:55393207..55395340,2	K562	blood:
3	chr2:55275064..55280479-chr2:55390367..55395295,9	MCF-7	breast:
4	chr2:55274543..55277923-chr2:55387934..55394752,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10172326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193022	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10197309	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1133181	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1133182	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11679663	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs11685292	0.81[EUR][1000 genomes]
rs12621144	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13012766	0.87[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs13013134	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs13019355	0.86[ASN][1000 genomes]
rs13021215	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13023235	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13417057	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14026	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1437391	0.89[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs2164714	0.82[CEU][hapmap]
rs2576710	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap]
rs35026006	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35890669	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3935223	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4420737	0.83[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4671241	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671242	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4672026	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4672027	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56095114	0.87[AFR][1000 genomes]
rs6545474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545475	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545478	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6714830	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595134	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6759911	C2orf63	cis	cerebellum	SCAN
rs6759911	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55383600-55395600	Enhancers	Pancreas	Pancrea
2	chr2:55386000-55395000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
4	chr2:55387400-55395600	Enhancers	Lung	lung
5	chr2:55387600-55395000	Weak transcription	Psoas Muscle	Psoas
6	chr2:55388000-55395200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55388800-55395000	Weak transcription	Left Ventricle	heart
8	chr2:55389000-55394800	Enhancers	Brain Cingulate Gyrus	brain
9	chr2:55389000-55394800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:55389200-55394000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:55389200-55394800	Enhancers	Brain Anterior Caudate	brain
12	chr2:55389200-55397400	Enhancers	NHLF	lung
13	chr2:55389400-55394800	Enhancers	Brain Hippocampus Middle	brain
14	chr2:55389400-55395200	Weak transcription	NHEK	skin
15	chr2:55389800-55394000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55389800-55394600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:55389800-55395000	Weak transcription	Brain Germinal Matrix	brain
18	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
19	chr2:55390000-55395600	Enhancers	Ovary	ovary
20	chr2:55390200-55394800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:55390200-55395200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:55390400-55394000	Enhancers	Fetal Intestine Small	intestine
23	chr2:55390400-55394800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:55390400-55395000	Weak transcription	Fetal Thymus	thymus
25	chr2:55390400-55395200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:55390400-55395600	Enhancers	Right Atrium	heart
27	chr2:55390600-55395800	Enhancers	K562	blood
28	chr2:55390800-55394600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:55391000-55394800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:55391000-55395400	Weak transcription	Spleen	Spleen
31	chr2:55391000-55397000	Enhancers	Brain Angular Gyrus	brain
32	chr2:55391200-55394000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:55391200-55394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:55391200-55394600	Weak transcription	Fetal Stomach	stomach
35	chr2:55391200-55395000	Enhancers	Brain Substantia Nigra	brain
36	chr2:55391200-55397000	Enhancers	NHDF-Ad	bronchial
37	chr2:55391400-55394600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:55391400-55394600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:55391400-55395000	Weak transcription	Aorta	Aorta
40	chr2:55391400-55395800	Enhancers	Stomach Mucosa	stomach
41	chr2:55391600-55394800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:55391800-55394000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:55391800-55394200	Enhancers	Fetal Intestine Large	intestine
44	chr2:55392000-55394600	Weak transcription	Fetal Lung	lung
45	chr2:55392000-55394800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:55392000-55395000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:55392000-55395400	Weak transcription	Fetal Brain Male	brain
48	chr2:55392000-55397400	Enhancers	HSMM	muscle
49	chr2:55392200-55394600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:55392200-55394800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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