Variant report

Variant	rs2297419
Chromosome Location	chr1:227182754-227182755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227160421..227162343-chr1:227181472..227183178,2	MCF-7	breast:
2	chr1:227129636..227132325-chr1:227181300..227183713,2	K562	blood:
3	chr1:227182754..227185276-chr1:227188097..227190742,3	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10127638	0.81[CEU][hapmap]
rs1045285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1045287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10495256	0.81[CEU][hapmap]
rs10916075	0.99[ASN][1000 genomes]
rs11577007	0.99[ASN][1000 genomes]
rs11578103	0.99[ASN][1000 genomes]
rs11578479	0.89[ASN][1000 genomes]
rs11580229	0.89[ASN][1000 genomes]
rs11583229	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11583489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11588329	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11588904	0.99[ASN][1000 genomes]
rs12403236	0.99[ASN][1000 genomes]
rs12403775	0.90[CHB][hapmap]
rs12405857	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12406714	0.99[ASN][1000 genomes]
rs12409230	0.93[ASN][1000 genomes]
rs12409428	0.99[ASN][1000 genomes]
rs12409755	0.99[ASN][1000 genomes]
rs12410103	0.99[ASN][1000 genomes]
rs12593	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1319103	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1343743	0.99[ASN][1000 genomes]
rs1343744	0.99[ASN][1000 genomes]
rs1343745	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600725	0.89[ASN][1000 genomes]
rs17600747	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17600947	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1929855	0.80[CEU][hapmap];0.93[CHB][hapmap]
rs1929863	0.99[ASN][1000 genomes]
rs1929864	0.99[ASN][1000 genomes]
rs2104860	0.89[ASN][1000 genomes]
rs2297413	0.95[EUR][1000 genomes]
rs2297415	0.95[ASN][1000 genomes]
rs2297416	0.93[ASN][1000 genomes]
rs2297418	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2802271	0.81[CEU][hapmap]
rs3738729	0.99[ASN][1000 genomes]
rs3768419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3768420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768423	0.99[ASN][1000 genomes]
rs3795445	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3795446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3795449	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3795453	0.89[ASN][1000 genomes]
rs4146588	0.81[CEU][hapmap];0.93[CHB][hapmap]
rs61834001	0.99[ASN][1000 genomes]
rs61834006	0.97[ASN][1000 genomes]
rs61834039	0.88[ASN][1000 genomes]
rs6426559	0.99[ASN][1000 genomes]
rs6426560	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6426584	0.93[CHB][hapmap]
rs6659424	0.96[ASN][1000 genomes]
rs6664955	0.99[ASN][1000 genomes]
rs6670924	0.99[ASN][1000 genomes]
rs6677602	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6684821	0.99[ASN][1000 genomes]
rs6693535	0.99[ASN][1000 genomes]
rs7535826	0.89[ASN][1000 genomes]
rs7541033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7549465	0.85[ASN][1000 genomes]
rs7549586	0.89[ASN][1000 genomes]
rs7553837	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7555621	0.84[ASN][1000 genomes]
rs938257	0.81[CEU][hapmap]
rs9726097	0.99[ASN][1000 genomes]
rs9727512	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297419	CAPN2	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:227175200-227198400	Weak transcription	A549	lung
6	chr1:227175200-227210200	Weak transcription	HMEC	breast
7	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
10	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:227176000-227216400	Weak transcription	NHLF	lung
12	chr1:227176400-227190400	Weak transcription	Osteobl	bone
13	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:227177200-227188600	Weak transcription	Fetal Lung	lung
15	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
16	chr1:227178000-227183200	Strong transcription	Fetal Stomach	stomach
17	chr1:227178200-227183000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:227178200-227188600	Weak transcription	HSMMtube	muscle
19	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
21	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:227178800-227183000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:227178800-227188800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:227179000-227182800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:227179000-227188400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:227179400-227183000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:227179400-227183200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:227179400-227188200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
32	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
33	chr1:227179600-227213800	Weak transcription	NH-A	brain
34	chr1:227180000-227183200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:227180200-227183200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:227180200-227184200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:227180400-227183000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227180400-227184600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:227180600-227183000	Strong transcription	Liver	Liver
40	chr1:227180600-227183200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:227180600-227183200	Strong transcription	Pancreas	Pancrea
42	chr1:227180800-227183200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:227180800-227187800	Weak transcription	HSMM	muscle
44	chr1:227180800-227190200	Weak transcription	K562	blood
45	chr1:227181000-227183000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:227181200-227190400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:227181400-227184000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:227181600-227183200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:227181600-227183400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:227181600-227184000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links