Variant report

Variant	rs872588
Chromosome Location	chr13:111015877-111015878
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1888004	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1888005	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773169	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773170	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773171	0.86[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773173	0.93[ASW][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7318424	0.93[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7333596	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7333748	0.86[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7334022	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs750598	0.94[JPT][hapmap];0.81[YRI][hapmap]
rs7999034	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs872587	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs872589	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs913746	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9515195	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9515196	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9515197	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515199	0.83[JPT][hapmap]
rs9521717	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9521718	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9521719	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9521720	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9521721	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9521730	0.94[JPT][hapmap]
rs9521732	0.84[JPT][hapmap]
rs9521733	0.84[JPT][hapmap]
rs952359	1.00[JPT][hapmap]
rs9555692	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9555694	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9559780	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9559781	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[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	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110994000-111019600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:111000800-111019800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:111002400-111026000	Weak transcription	Psoas Muscle	Psoas
4	chr13:111007400-111023000	Weak transcription	A549	lung
5	chr13:111007600-111020400	Weak transcription	Fetal Kidney	kidney
6	chr13:111007600-111030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:111007600-111031000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:111007600-111031400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:111007800-111018000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:111008400-111020000	Weak transcription	HMEC	breast
11	chr13:111008600-111018000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:111009000-111018000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr13:111009000-111024000	Weak transcription	Pancreas	Pancrea
14	chr13:111009000-111029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:111009800-111016200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:111009800-111018400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:111010200-111016000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:111010400-111024000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:111011000-111016400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr13:111011000-111016800	Weak transcription	Fetal Intestine Large	intestine
21	chr13:111011000-111022000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:111011000-111024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:111011000-111032000	Weak transcription	Gastric	stomach
24	chr13:111011000-111032400	Weak transcription	NHEK	skin
25	chr13:111011200-111016800	Enhancers	Colon Smooth Muscle	Colon
26	chr13:111011200-111029800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr13:111011400-111016600	Enhancers	Rectal Smooth Muscle	rectum
28	chr13:111011800-111016200	Enhancers	Right Ventricle	heart
29	chr13:111011800-111016400	Enhancers	Left Ventricle	heart
30	chr13:111011800-111016800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr13:111012000-111016000	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr13:111012000-111016800	Enhancers	Right Atrium	heart
33	chr13:111012400-111016800	Enhancers	Ovary	ovary
34	chr13:111013800-111016000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:111013800-111017200	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr13:111013800-111023400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr13:111014000-111018000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr13:111014200-111017200	Genic enhancers	Fetal Muscle Leg	muscle
39	chr13:111014200-111019000	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:111014200-111019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:111014200-111024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:111014200-111027400	Weak transcription	Spleen	Spleen
43	chr13:111014400-111017800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:111014400-111018000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr13:111014400-111020000	Weak transcription	Fetal Lung	lung
46	chr13:111014400-111025800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr13:111014400-111029000	Weak transcription	HSMM	muscle
48	chr13:111014600-111017400	Strong transcription	Osteobl	bone
49	chr13:111014600-111017800	Weak transcription	Lung	lung
50	chr13:111014600-111018800	Weak transcription	HSMMtube	muscle

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