Variant report

Variant	rs13412513
Chromosome Location	chr2:233593337-233593338
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233591305..233594002-chr2:233611275..233613408,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHD1-2	chr2:233593258-233595607	NONHSAT077444

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10176930	0.80[ASN][1000 genomes]
rs10190211	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207739	0.84[ASN][1000 genomes]
rs10209575	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10933407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10933408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11679581	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11684636	0.84[ASN][1000 genomes]
rs11685169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11687379	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11688622	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688691	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11689661	0.84[ASN][1000 genomes]
rs11694434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695762	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052869	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694915	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12694916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12988087	0.80[AMR][1000 genomes]
rs13386650	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13396293	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13401578	0.90[ASN][1000 genomes]
rs13408229	0.84[ASN][1000 genomes]
rs13412034	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13425525	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429857	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1446307	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289914	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289915	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305139	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28491817	0.80[EUR][1000 genomes]
rs34063802	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34832091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35778045	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35785837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35928329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41266951	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56054779	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62193305	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6747479	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73005582	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7557131	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7564554	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9288675	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288676	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9808146	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9973586	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233564200-233596400	Weak transcription	NHLF	lung
2	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
4	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
5	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
6	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
8	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
10	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:233570600-233593400	Weak transcription	Aorta	Aorta
13	chr2:233571200-233593600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
15	chr2:233571200-233627400	Weak transcription	Gastric	stomach
16	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
17	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:233574400-233593400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:233580000-233606000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:233580200-233596000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:233580600-233604000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:233580800-233595200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:233581000-233594200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:233585400-233595000	Strong transcription	HepG2	liver
26	chr2:233585600-233595000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:233585600-233595200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:233585800-233604400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:233585800-233626000	Weak transcription	Fetal Heart	heart
30	chr2:233586400-233595800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:233586400-233603200	Strong transcription	Fetal Thymus	thymus
32	chr2:233586400-233612200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:233586800-233599000	Weak transcription	K562	blood
34	chr2:233587000-233630600	Weak transcription	Psoas Muscle	Psoas
35	chr2:233587200-233596600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:233587200-233604400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:233587200-233613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:233587400-233594200	Weak transcription	Ovary	ovary
39	chr2:233587400-233594200	Weak transcription	Right Ventricle	heart
40	chr2:233588400-233595000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:233588400-233595200	Strong transcription	Fetal Stomach	stomach
42	chr2:233588400-233599600	Strong transcription	Primary T cells from cord blood	blood
43	chr2:233588600-233595000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:233588600-233595600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:233588600-233597000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:233588800-233595000	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:233588800-233595000	Strong transcription	GM12878-XiMat	blood
48	chr2:233588800-233596400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:233588800-233597000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:233588800-233605000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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