Variant report

Variant	rs2270856
Chromosome Location	chr2:234741808-234741809
allele	C/T
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	chr2:234389169..234389811-chr2:234741540..234742123,2	MCF-7	breast:
2	chr2:234312633..234313516-chr2:234741267..234742065,2	MCF-7	breast:
3	chr2:234614862..234617067-chr2:234739874..234742811,2	MCF-7	breast:
4	chr2:234607784..234610773-chr2:234739083..234742311,4	MCF-7	breast:
5	chr2:234736743..234738752-chr2:234740641..234743025,2	MCF-7	breast:
6	chr2:234388813..234389712-chr2:234741180..234742155,6	MCF-7	breast:
7	chr2:234738464..234743191-chr2:234754553..234759702,7	K562	blood:
8	chr2:234388065..234390771-chr2:234740107..234742680,2	MCF-7	breast:
9	chr2:234599519..234601666-chr2:234740030..234742555,2	MCF-7	breast:
10	chr2:234741715..234743297-chr2:234743662..234746338,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185038	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000123485	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10185631	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11563015	0.85[JPT][hapmap]
rs11563235	0.84[CHB][hapmap]
rs11563240	0.85[JPT][hapmap]
rs13415293	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13416326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270854	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2361507	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755317	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876020	chr2:234724225-234748814	Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv876021	chr2:234725819-234748814	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv876022	chr2:234726154-234748814	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv876023	chr2:234726154-234763137	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1008316	chr2:234728911-234758539	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv961012	chr2:234740682-234742127	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2270856	FGD5	trans	lymphoblastoid	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234732200-234742000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:234733400-234742200	Weak transcription	Liver	Liver
3	chr2:234736400-234762600	Weak transcription	Right Atrium	heart
4	chr2:234738200-234744000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:234738200-234762000	Weak transcription	Esophagus	oesophagus
6	chr2:234738800-234743000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:234738800-234744000	Weak transcription	NHLF	lung
8	chr2:234739000-234742600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:234739000-234742600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:234739200-234742600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:234739200-234743000	Weak transcription	HepG2	liver
12	chr2:234739400-234742600	Enhancers	Fetal Muscle Trunk	muscle
13	chr2:234739400-234744000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:234739600-234747600	Weak transcription	Brain Germinal Matrix	brain
15	chr2:234739800-234742600	Enhancers	Fetal Muscle Leg	muscle
16	chr2:234739800-234752800	Weak transcription	Spleen	Spleen
17	chr2:234740000-234742400	Weak transcription	Fetal Thymus	thymus
18	chr2:234740000-234760000	Strong transcription	Thymus	Thymus
19	chr2:234740200-234742600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:234740200-234742800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:234740200-234743000	Weak transcription	HMEC	breast
22	chr2:234740200-234761000	Weak transcription	Primary B cells from cord blood	blood
23	chr2:234740400-234762200	Weak transcription	Primary T cells from cord blood	blood
24	chr2:234740600-234742200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:234740600-234742600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:234740600-234742600	Weak transcription	GM12878-XiMat	blood
27	chr2:234740600-234743600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:234740800-234742200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:234740800-234742600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:234740800-234742600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:234740800-234743400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:234741000-234742200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr2:234741000-234742200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:234741000-234742400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:234741000-234742800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:234741000-234742800	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:234741000-234742800	Weak transcription	K562	blood
38	chr2:234741000-234742800	Weak transcription	NHDF-Ad	bronchial
39	chr2:234741000-234743800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:234741200-234742000	Enhancers	Fetal Intestine Small	intestine
41	chr2:234741200-234742200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:234741200-234742800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:234741200-234743000	Enhancers	Adipose Nuclei	Adipose
44	chr2:234741200-234744400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:234741200-234759800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:234741400-234742000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:234741400-234742000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:234741400-234742000	Enhancers	Duodenum Mucosa	Duodenum
49	chr2:234741400-234742000	Enhancers	Fetal Intestine Large	intestine
50	chr2:234741400-234742200	Enhancers	Fetal Lung	lung

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