Variant report

Variant	rs13092935
Chromosome Location	chr3:139175464-139175465
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	chr3:139168645..139171256-chr3:139173067..139176313,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1044826	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10460845	0.87[ASN][1000 genomes]
rs10935320	0.88[ASN][1000 genomes]
rs10935323	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488939	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12494556	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12494806	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12695698	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695700	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13060697	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13071857	0.80[EUR][1000 genomes]
rs13074208	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083195	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085888	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13086868	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13089007	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089052	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13089090	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13092507	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1586861	0.88[ASN][1000 genomes]
rs1586863	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586864	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17336869	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1907687	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165139	0.92[ASN][1000 genomes]
rs2233811	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2233815	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2349059	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34623690	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772877	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772878	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772879	0.97[ASN][1000 genomes]
rs3821544	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821545	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4544576	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683818	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67929453	0.90[ASN][1000 genomes]
rs7374385	0.91[EUR][1000 genomes]
rs747346	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9289578	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964227	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs973691	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818691	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9825064	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9831108	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834607	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835241	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848241	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9849039	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9849578	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853350	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9860201	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9860521	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9868544	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882014	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
2	chr3:139154200-139178600	Weak transcription	Left Ventricle	heart
3	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
4	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:139165800-139178600	Weak transcription	Right Ventricle	heart
6	chr3:139166000-139179000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:139167400-139176000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:139168600-139196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:139171200-139210200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:139171400-139175800	Weak transcription	Brain Substantia Nigra	brain
11	chr3:139171400-139179400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr3:139171400-139179400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:139171800-139176000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:139171800-139176200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:139172000-139175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:139172000-139176200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:139172000-139176200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:139172400-139177000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:139173400-139175600	Genic enhancers	Fetal Intestine Large	intestine
20	chr3:139173800-139178400	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:139173800-139180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:139173800-139180600	Weak transcription	Pancreas	Pancrea
23	chr3:139174200-139176800	Enhancers	Ovary	ovary
24	chr3:139174600-139176200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:139174600-139177200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:139174800-139175600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:139174800-139176400	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:139174800-139176800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:139174800-139176800	Enhancers	HMEC	breast
30	chr3:139174800-139177000	Enhancers	NHEK	skin
31	chr3:139174800-139177200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:139175000-139175600	Weak transcription	Fetal Intestine Small	intestine
33	chr3:139175000-139175800	Weak transcription	Esophagus	oesophagus
34	chr3:139175200-139176000	Enhancers	Brain Angular Gyrus	brain
35	chr3:139175400-139175600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:139175400-139176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:139175400-139176800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:139175400-139178600	Weak transcription	Adipose Nuclei	Adipose
39	chr3:139175400-139179400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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