Variant report

Variant	rs3755264
Chromosome Location	chr2:10546236-10546237
allele	A/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10464962..10467287-chr2:10544928..10546718,2	MCF-7	breast:
2	chr2:10261171..10265935-chr2:10544190..10551018,10	K562	blood:
3	chr2:10440924..10446095-chr2:10544022..10551736,19	MCF-7	breast:
4	chr2:10543950..10547023-chr2:10547884..10550475,4	MCF-7	breast:
5	chr2:10544615..10547096-chr2:10548655..10551250,3	K562	blood:
6	chr2:10535464..10537756-chr2:10546210..10548957,2	K562	blood:
7	chr2:10499610..10502140-chr2:10544416..10546465,2	K562	blood:
8	chr2:10272230..10274773-chr2:10544365..10546593,2	MCF-7	breast:
9	chr2:10410506..10411312-chr2:10545626..10546272,2	MCF-7	breast:
10	chr2:10539665..10541710-chr2:10544795..10547261,2	MCF-7	breast:
11	chr2:10518586..10521002-chr2:10545177..10547256,3	MCF-7	breast:
12	chr2:10410711..10412312-chr2:10545552..10547500,2	K562	blood:
13	chr2:10441653..10444560-chr2:10544064..10547799,5	MCF-7	breast:
14	chr2:10397007..10398752-chr2:10545824..10548279,2	MCF-7	breast:
15	chr2:10538831..10544260-chr2:10544573..10548851,6	K562	blood:
16	chr2:10270635..10275854-chr2:10544682..10552679,11	K562	blood:
17	chr2:10546025..10548259-chr2:10592640..10594576,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115756	Chromatin interaction
ENSG00000171848	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10189719	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467741	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472775	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808315	0.94[ASN][1000 genomes]
rs2270299	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2270300	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2270301	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs35158739	0.85[ASN][1000 genomes]
rs3755263	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771128	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771129	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3771134	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771141	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771147	0.90[CEU][hapmap]
rs62130186	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62130189	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62130190	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs876614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876615	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs876616	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];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	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755264	C2orf48	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10533000-10551800	Weak transcription	Ovary	ovary
2	chr2:10533400-10549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:10541000-10547400	Weak transcription	K562	blood
4	chr2:10541200-10550800	Enhancers	Fetal Muscle Leg	muscle
5	chr2:10541800-10546400	Enhancers	Adipose Nuclei	Adipose
6	chr2:10541800-10546400	Weak transcription	Fetal Thymus	thymus
7	chr2:10541800-10547200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:10542000-10546400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:10542000-10546600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:10542000-10547000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:10542000-10549400	Enhancers	HUVEC	blood vessel
12	chr2:10542200-10547600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:10542400-10546400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:10542400-10549400	Enhancers	NHDF-Ad	bronchial
15	chr2:10542600-10546400	Weak transcription	Primary B cells from cord blood	blood
16	chr2:10542600-10546400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:10542800-10546600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:10542800-10547000	Weak transcription	Small Intestine	intestine
19	chr2:10543000-10546800	Weak transcription	Colonic Mucosa	Colon
20	chr2:10543200-10546400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:10543400-10547600	Weak transcription	HepG2	liver
22	chr2:10543600-10546800	Strong transcription	Fetal Intestine Small	intestine
23	chr2:10544000-10547400	Strong transcription	Fetal Intestine Large	intestine
24	chr2:10544000-10548000	Enhancers	HMEC	breast
25	chr2:10544200-10546400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:10544200-10546400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:10544200-10546600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:10544200-10549600	Enhancers	Left Ventricle	heart
29	chr2:10544200-10549800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:10544400-10546400	Enhancers	Fetal Brain Male	brain
31	chr2:10544400-10546800	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr2:10544400-10547000	Enhancers	Brain Angular Gyrus	brain
33	chr2:10544400-10547000	Enhancers	Brain Anterior Caudate	brain
34	chr2:10544400-10547000	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:10544400-10547200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr2:10544400-10547400	Genic enhancers	Fetal Stomach	stomach
37	chr2:10544400-10548800	Enhancers	Esophagus	oesophagus
38	chr2:10544400-10549800	Enhancers	Right Ventricle	heart
39	chr2:10544600-10548000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:10544600-10548200	Bivalent Enhancer	Placenta	Placenta
41	chr2:10544600-10548600	Enhancers	Liver	Liver
42	chr2:10544600-10549400	Enhancers	Right Atrium	heart
43	chr2:10544800-10546400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:10544800-10547200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr2:10544800-10548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:10544800-10548800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:10544800-10549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:10544800-10549600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr2:10544800-10549800	Enhancers	Lung	lung
50	chr2:10545000-10546400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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