Variant report

Variant	rs1397575
Chromosome Location	chr9:94011892-94011893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94010552..94013353-chr9:94014239..94017543,3	K562	blood:
2	chr9:94010195..94012758-chr9:94017416..94020227,2	MCF-7	breast:
3	chr9:94006388..94008643-chr9:94010253..94011944,2	MCF-7	breast:
4	chr9:94009034..94011977-chr9:94185293..94186951,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165030	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10991837	0.91[EUR][1000 genomes]
rs10991848	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10991849	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10991853	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10991880	0.90[ASN][1000 genomes]
rs10991882	0.86[EUR][1000 genomes]
rs10991900	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs12683737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1331691	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16907358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16907394	0.86[EUR][1000 genomes]
rs1848984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877125	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55642352	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59727648	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479337	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs7019926	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7020893	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs7028794	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7031965	0.83[EUR][1000 genomes]
rs7849152	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7852888	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7856089	0.86[CHB][hapmap]
rs7857616	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7866204	0.91[EUR][1000 genomes]
rs7868501	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7868771	0.86[CHB][hapmap]
rs9792678	0.88[EUR][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	nsv893570	chr9:93973938-94148084	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482877	chr9:93979351-94157734	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1397575	ECM2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93982800-94032400	Weak transcription	Ovary	ovary
2	chr9:93983000-94027000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:93983000-94054000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:93983200-94015400	Weak transcription	Thymus	Thymus
5	chr9:93983200-94015800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:93983200-94027800	Weak transcription	Adipose Nuclei	Adipose
7	chr9:93984000-94052200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:93984000-94054600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:93984200-94024000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:93984400-94026200	Weak transcription	Primary T cells from cord blood	blood
11	chr9:93995800-94018600	Weak transcription	Fetal Intestine Small	intestine
12	chr9:93995800-94052400	Weak transcription	Fetal Stomach	stomach
13	chr9:93996800-94012400	Weak transcription	HSMMtube	muscle
14	chr9:93999200-94015800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:94002800-94032600	Weak transcription	Placenta	Placenta
16	chr9:94004600-94051800	Weak transcription	Liver	Liver
17	chr9:94006000-94015800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:94008000-94013200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr9:94008200-94013600	Enhancers	Fetal Heart	heart
20	chr9:94008400-94018600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:94008400-94018600	Weak transcription	Esophagus	oesophagus
22	chr9:94008600-94036200	Weak transcription	HSMM	muscle
23	chr9:94008800-94017800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:94009000-94012600	Weak transcription	HepG2	liver
25	chr9:94009400-94015000	Weak transcription	Hela-S3	cervix
26	chr9:94009400-94017000	Weak transcription	NHDF-Ad	bronchial
27	chr9:94009400-94022400	Weak transcription	Fetal Brain Female	brain
28	chr9:94009600-94020400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:94009800-94012400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:94009800-94012400	Weak transcription	Fetal Muscle Leg	muscle
31	chr9:94009800-94013400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:94009800-94018600	Weak transcription	Lung	lung
33	chr9:94009800-94018600	Weak transcription	Pancreas	Pancrea
34	chr9:94009800-94018800	Weak transcription	Right Ventricle	heart
35	chr9:94010000-94021600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr9:94010000-94031600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:94011400-94013400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:94011400-94055400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:94011600-94013400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:94011600-94015800	Weak transcription	Left Ventricle	heart
41	chr9:94011600-94018600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:94011600-94018600	Weak transcription	Right Atrium	heart
43	chr9:94011600-94019600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr9:94011800-94012200	Weak transcription	Psoas Muscle	Psoas
45	chr9:94011800-94012200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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