Variant report

Variant	rs56670003
Chromosome Location	chr15:42548434-42548435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42547199..42549905-chr15:42563424..42565633,2	K562	blood:
2	chr15:42545753..42549905-chr15:42563424..42566580,4	K562	blood:
3	chr15:42544015..42546634-chr15:42547457..42549970,2	K562	blood:

Variant related genes	Relation type
ENSG00000103978	Chromatin interaction
ENSG00000214013	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10220859	0.81[AMR][1000 genomes]
rs12437600	0.92[ASN][1000 genomes]
rs12438369	0.84[ASN][1000 genomes]
rs12438509	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440087	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441016	0.94[ASN][1000 genomes]
rs12441642	0.84[ASN][1000 genomes]
rs1659213	0.84[AMR][1000 genomes]
rs1659218	0.87[AMR][1000 genomes]
rs1659219	0.87[AMR][1000 genomes]
rs1659221	0.87[AMR][1000 genomes]
rs1659222	0.87[AMR][1000 genomes]
rs1678984	0.87[AMR][1000 genomes]
rs1678992	0.87[AMR][1000 genomes]
rs1678993	0.81[AMR][1000 genomes]
rs16972770	0.83[AMR][1000 genomes]
rs16972776	0.85[AMR][1000 genomes]
rs16972887	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973008	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973045	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16973060	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2138831	0.86[ASN][1000 genomes]
rs2407707	0.89[ASN][1000 genomes]
rs2412688	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28364388	0.84[ASN][1000 genomes]
rs2918460	0.87[AMR][1000 genomes]
rs3736099	0.89[ASN][1000 genomes]
rs3743005	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3743007	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3743008	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3825785	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4506867	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4923932	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923945	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924627	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924630	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924631	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4924644	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924672	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924673	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924674	0.84[ASN][1000 genomes]
rs55882551	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56257215	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56702977	0.84[ASN][1000 genomes]
rs56987883	0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57134130	0.84[ASN][1000 genomes]
rs57393446	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57933952	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57973092	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57976413	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58292736	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58313689	0.92[ASN][1000 genomes]
rs58712370	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59094161	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59132828	0.95[ASN][1000 genomes]
rs59138723	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59320762	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59893734	0.89[ASN][1000 genomes]
rs59974698	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60443443	0.89[ASN][1000 genomes]
rs60506946	0.83[AMR][1000 genomes]
rs60634548	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61069354	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61133768	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6493033	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179203	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7180279	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7181979	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73398938	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400993	0.89[ASN][1000 genomes]
rs73402707	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73403365	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73403545	0.80[AMR][1000 genomes]
rs73403546	0.83[AMR][1000 genomes]
rs73403548	0.84[AMR][1000 genomes]
rs73403550	0.83[AMR][1000 genomes]
rs73407403	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407407	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407488	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409577	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74009020	0.81[AMR][1000 genomes]
rs8025601	0.95[ASN][1000 genomes]
rs8027016	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041951	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv1006302	chr15:42545749-42552598	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42519400-42562800	Weak transcription	Fetal Heart	heart
3	chr15:42520200-42561000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:42521000-42551000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:42528800-42548800	Weak transcription	Small Intestine	intestine
6	chr15:42530600-42548800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:42530800-42551600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:42530800-42551600	Weak transcription	Right Ventricle	heart
9	chr15:42531800-42551800	Weak transcription	Psoas Muscle	Psoas
10	chr15:42532000-42551600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:42532200-42551000	Weak transcription	HMEC	breast
12	chr15:42532200-42552800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:42542800-42550000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:42542800-42561600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:42543400-42551000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr15:42543400-42559000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:42543400-42561200	Strong transcription	Liver	Liver
18	chr15:42543600-42548600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr15:42543600-42552600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:42543600-42561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr15:42543800-42549600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr15:42543800-42552800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:42543800-42556600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:42543800-42557000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:42543800-42560200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr15:42543800-42560800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr15:42543800-42561600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr15:42544000-42560600	Strong transcription	Adipose Nuclei	Adipose
29	chr15:42544000-42560800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:42544200-42561000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:42544200-42561200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr15:42544200-42561200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:42544200-42561800	Strong transcription	Osteobl	bone
34	chr15:42544400-42548800	Weak transcription	Left Ventricle	heart
35	chr15:42544400-42549000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:42544400-42549600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
37	chr15:42544400-42561200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:42544400-42561200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:42544600-42548800	Weak transcription	Aorta	Aorta
40	chr15:42544600-42549000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:42544600-42550600	Weak transcription	Gastric	stomach
42	chr15:42544600-42550800	Weak transcription	Spleen	Spleen
43	chr15:42544600-42551600	Weak transcription	Esophagus	oesophagus
44	chr15:42544600-42551600	Weak transcription	Pancreas	Pancrea
45	chr15:42544600-42557800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:42544600-42560600	Strong transcription	Placenta	Placenta
47	chr15:42544600-42560800	Strong transcription	Fetal Thymus	thymus
48	chr15:42544600-42561600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:42544800-42559800	Strong transcription	Fetal Kidney	kidney
50	chr15:42544800-42560800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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