Variant report

Variant	rs1892490
Chromosome Location	chr1:227150266-227150267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227126882..227129582-chr1:227150200..227152334,2	K562	blood:
2	chr1:227126954..227128546-chr1:227148554..227151462,2	MCF-7	breast:
3	chr1:227149071..227151411-chr1:227152108..227154621,2	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
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];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]
rs2777832	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2802277	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]
rs35606438	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3425052	chr1:227145829-227150327	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1892490	CABC1	cis	parietal	SCAN
rs1892490	SNAP47	cis	cerebellum	SCAN
rs1892490	LIN9	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

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	chr1:227131400-227153800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:227134400-227151800	Weak transcription	Small Intestine	intestine
6	chr1:227134400-227153000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227135000-227150600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:227135200-227152600	Weak transcription	Colonic Mucosa	Colon
9	chr1:227135200-227158000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:227136200-227152800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:227137400-227150400	Weak transcription	Aorta	Aorta
12	chr1:227138000-227152000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:227139200-227151600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:227139400-227150600	Weak transcription	Primary B cells from cord blood	blood
15	chr1:227140000-227152200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:227140000-227152800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:227140000-227153000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:227142200-227157800	Weak transcription	Fetal Lung	lung
19	chr1:227142800-227152200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:227143000-227153800	Weak transcription	Hela-S3	cervix
21	chr1:227143400-227161200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:227145400-227159600	Weak transcription	Brain Substantia Nigra	brain
23	chr1:227145800-227151600	Weak transcription	Brain Anterior Caudate	brain
24	chr1:227146000-227152000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:227146200-227150800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:227146400-227162600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:227146600-227151400	Weak transcription	Liver	Liver
28	chr1:227146800-227152800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:227147000-227152200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:227147200-227161000	Weak transcription	Stomach Mucosa	stomach
32	chr1:227147400-227156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:227147800-227158600	Strong transcription	Primary T cells from cord blood	blood
34	chr1:227148200-227151600	Strong transcription	HepG2	liver
35	chr1:227148200-227153400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:227148200-227162000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:227148400-227150800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227148400-227152000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:227148400-227153000	Weak transcription	Dnd41	blood
40	chr1:227148400-227156400	Strong transcription	Fetal Intestine Small	intestine
41	chr1:227148400-227156600	Strong transcription	Fetal Stomach	stomach
42	chr1:227148400-227159400	Weak transcription	A549	lung
43	chr1:227148600-227150800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:227148600-227150800	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:227148600-227151200	Strong transcription	Thymus	Thymus
46	chr1:227148600-227152600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:227148600-227158400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:227148800-227151400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:227148800-227152000	Weak transcription	Fetal Brain Female	brain

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