Variant report

Variant	rs2802277
Chromosome Location	chr1:227154233-227154234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227154071..227157064-chr1:227173659..227175478,2	MCF-7	breast:
2	chr1:227127006..227129793-chr1:227152681..227157136,4	K562	blood:
3	chr1:227154208..227155807-chr1:227178549..227181040,2	K562	blood:
4	chr1:227127006..227129675-chr1:227153566..227157136,5	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction
ENSG00000233706	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1892490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2154367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777832	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35606438	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873236	chr1:227118912-227173537	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2802277	SNAP47	cis	cerebellum	SCAN
rs2802277	CABC1	cis	parietal	SCAN
rs2802277	LIN9	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227129000-227162600	Weak transcription	Fetal Kidney	kidney
2	chr1:227130400-227154600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:227131000-227171800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:227135200-227158000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:227142200-227157800	Weak transcription	Fetal Lung	lung
6	chr1:227143400-227161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:227145400-227159600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:227146400-227162600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:227147200-227161000	Weak transcription	Stomach Mucosa	stomach
11	chr1:227147400-227156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:227147800-227158600	Strong transcription	Primary T cells from cord blood	blood
13	chr1:227148200-227162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:227148400-227156400	Strong transcription	Fetal Intestine Small	intestine
15	chr1:227148400-227156600	Strong transcription	Fetal Stomach	stomach
16	chr1:227148400-227159400	Weak transcription	A549	lung
17	chr1:227148600-227158400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:227149000-227157600	Weak transcription	K562	blood
20	chr1:227149000-227158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:227149200-227154800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:227149200-227156600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:227149200-227158400	Strong transcription	Ovary	ovary
24	chr1:227149400-227155200	Strong transcription	Gastric	stomach
25	chr1:227149400-227156400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:227149400-227158400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:227149400-227161600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:227149800-227154600	Strong transcription	Esophagus	oesophagus
29	chr1:227149800-227155400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:227150000-227155400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:227150000-227155800	Genic enhancers	Left Ventricle	heart
32	chr1:227150200-227154400	Genic enhancers	Right Ventricle	heart
33	chr1:227150200-227158400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:227150400-227154400	Strong transcription	Aorta	Aorta
35	chr1:227150400-227158000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:227150400-227159600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:227150800-227159400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:227151200-227158000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:227151200-227158200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:227151400-227159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:227151600-227154800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:227151600-227155400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:227151800-227159400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:227152000-227154400	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:227152000-227154600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:227152000-227154600	Strong transcription	Fetal Brain Female	brain
47	chr1:227152000-227155000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:227152000-227156200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:227152000-227156800	Strong transcription	Fetal Intestine Large	intestine
50	chr1:227152200-227154600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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