Variant report

Variant	rs13397060
Chromosome Location	chr2:128624998-128624999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128617356..128621045-chr2:128621951..128625083,3	MCF-7	breast:
2	chr2:128615903..128617579-chr2:128623760..128626611,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10171898	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10210695	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11557685	1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs11674513	0.81[ASN][1000 genomes]
rs11678032	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11692524	1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs11693759	1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13421835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423029	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17418125	0.81[ASN][1000 genomes]
rs17534053	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17534123	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17599575	1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs17600177	1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs3771291	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs56954978	0.81[ASN][1000 genomes]
rs57498556	0.81[ASN][1000 genomes]
rs57913162	0.81[ASN][1000 genomes]
rs57986825	0.81[ASN][1000 genomes]
rs58080260	0.81[ASN][1000 genomes]
rs59009188	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs59090605	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59727076	0.81[ASN][1000 genomes]
rs59918187	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60087786	0.81[ASN][1000 genomes]
rs61187878	0.81[ASN][1000 genomes]
rs61730415	0.81[ASN][1000 genomes]
rs6714620	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6734925	0.81[ASN][1000 genomes]
rs6749005	0.93[CEU][hapmap]
rs6756507	0.81[ASN][1000 genomes]
rs72963794	0.81[ASN][1000 genomes]
rs7560482	0.80[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574303	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575961	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7585200	0.81[ASN][1000 genomes]
rs7591477	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7605158	1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368061	chr2:128375044-128672849	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13397060	LOC401010	cis	cerebellum	SCAN
rs13397060	AMMECR1L	cis	parietal	SCAN
rs13397060	WDR33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128616200-128628400	Weak transcription	Fetal Brain Male	brain
2	chr2:128616200-128641400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:128617600-128626600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:128618000-128625200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:128618000-128627000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:128618000-128630200	Weak transcription	Right Atrium	heart
7	chr2:128619200-128631800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:128619600-128631600	Strong transcription	HSMM	muscle
9	chr2:128619600-128631800	Strong transcription	Primary B cells from cord blood	blood
10	chr2:128619800-128625800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:128619800-128629800	Strong transcription	Fetal Intestine Small	intestine
12	chr2:128619800-128630200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:128619800-128631600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:128619800-128631800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:128619800-128631800	Strong transcription	Thymus	Thymus
16	chr2:128619800-128631800	Strong transcription	A549	lung
17	chr2:128619800-128631800	Strong transcription	HMEC	breast
18	chr2:128619800-128631800	Strong transcription	NHLF	lung
19	chr2:128619800-128632000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:128619800-128632000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:128619800-128632200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:128619800-128632200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:128619800-128632600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:128619800-128632600	Strong transcription	Fetal Muscle Leg	muscle
25	chr2:128619800-128632800	Strong transcription	Fetal Intestine Large	intestine
26	chr2:128619800-128632800	Strong transcription	Fetal Stomach	stomach
27	chr2:128620000-128629400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:128620000-128630000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:128620000-128631800	Strong transcription	Osteobl	bone
30	chr2:128620000-128632200	Strong transcription	Primary T cells from cord blood	blood
31	chr2:128620000-128632400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:128620000-128632400	Strong transcription	Dnd41	blood
33	chr2:128620000-128632600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:128620000-128632600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:128620200-128625600	Strong transcription	Brain Germinal Matrix	brain
36	chr2:128620200-128626400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:128620200-128630000	Strong transcription	Fetal Thymus	thymus
38	chr2:128620200-128630200	Strong transcription	Liver	Liver
39	chr2:128620200-128630200	Strong transcription	Left Ventricle	heart
40	chr2:128620200-128630600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:128620200-128631400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:128620200-128631600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:128620200-128632600	Strong transcription	NHEK	skin
44	chr2:128620200-128632800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:128620400-128631800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:128620400-128631800	Strong transcription	Adipose Nuclei	Adipose
47	chr2:128620400-128632000	Strong transcription	Placenta	Placenta
48	chr2:128620400-128632400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:128620400-128632400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:128620600-128625800	Strong transcription	Brain Angular Gyrus	brain

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