Variant report

Variant	rs59799252
Chromosome Location	chr3:160142234-160142235
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160142215-160142595	K562	blood:	n/a	n/a
2	POLR2A	chr3:160139039-160157396	K562	blood:	n/a	n/a
3	POLR2A	chr3:160142232-160142455	K562	blood:	n/a	n/a
4	POLR2A	chr3:160142181-160142405	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:160142061-160142887	K562	blood:	n/a	n/a
6	POLR2A	chr3:160141944-160143237	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SMC4	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10513550	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920289	0.91[EUR][1000 genomes]
rs12233589	0.91[EUR][1000 genomes]
rs2275153	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305401	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33999879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736627	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3773371	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806629	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41272959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532176	0.81[ASN][1000 genomes]
rs55815116	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119270	0.91[EUR][1000 genomes]
rs56124988	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56150006	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343019	0.83[ASN][1000 genomes]
rs56396435	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56401539	0.98[EUR][1000 genomes]
rs57030267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57050097	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57277659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57285344	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57328745	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57555307	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58377812	0.86[AMR][1000 genomes]
rs58627305	0.91[EUR][1000 genomes]
rs58654032	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58776572	0.98[EUR][1000 genomes]
rs58915028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695030	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60066272	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60153357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60222090	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60517889	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60607858	0.98[EUR][1000 genomes]
rs60640467	0.87[AFR][1000 genomes]
rs60914777	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61066536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272169	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272171	0.84[AMR][1000 genomes]
rs62272176	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272179	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272180	0.91[EUR][1000 genomes]
rs62272181	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272185	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272187	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272188	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272190	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272191	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272193	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272197	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272198	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272207	0.91[EUR][1000 genomes]
rs62272231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272243	0.84[AMR][1000 genomes]
rs62272245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62272253	0.84[AMR][1000 genomes]
rs62272254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272780	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272781	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272783	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272785	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272788	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272790	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272793	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62272799	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62272804	0.83[ASN][1000 genomes]
rs62272805	0.83[ASN][1000 genomes]
rs62272806	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272831	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272833	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272836	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272838	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66769612	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66850724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68069205	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154564	0.84[AMR][1000 genomes]
rs73154582	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73154583	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs73154587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155914	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614701	0.91[EUR][1000 genomes]
rs7618017	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645798	0.91[EUR][1000 genomes]
rs7648832	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637414	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160119000-160144600	Weak transcription	Spleen	Spleen
2	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:160119400-160144400	Weak transcription	Pancreas	Pancrea
4	chr3:160119400-160144600	Weak transcription	Gastric	stomach
5	chr3:160119800-160144400	Weak transcription	Esophagus	oesophagus
6	chr3:160119800-160144600	Weak transcription	Lung	lung
7	chr3:160119800-160144600	Weak transcription	Ovary	ovary
8	chr3:160119800-160144600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
11	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
12	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
14	chr3:160121200-160144400	Weak transcription	Colonic Mucosa	Colon
15	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:160122000-160144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
23	chr3:160122600-160155000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:160122600-160156600	Strong transcription	K562	blood
25	chr3:160122800-160154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:160123000-160153600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:160123200-160155400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:160124000-160159000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:160124200-160152600	Strong transcription	Hela-S3	cervix
30	chr3:160124600-160155000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:160125000-160144400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:160125200-160159800	Strong transcription	HSMM	muscle
33	chr3:160127800-160154000	Strong transcription	HMEC	breast
34	chr3:160127800-160157000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr3:160128000-160154200	Strong transcription	Dnd41	blood
36	chr3:160128200-160152400	Strong transcription	GM12878-XiMat	blood
37	chr3:160128400-160157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:160128600-160158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:160129200-160144600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:160129400-160149200	Weak transcription	Brain Angular Gyrus	brain
41	chr3:160129600-160151400	Strong transcription	Osteobl	bone
42	chr3:160129600-160156600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:160129600-160157000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:160129800-160151600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:160130000-160155000	Strong transcription	Placenta	Placenta
46	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:160130200-160142800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr3:160130400-160154000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:160130400-160157400	Strong transcription	NH-A	brain
50	chr3:160131800-160143200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links