Variant report

Variant	rs244643
Chromosome Location	chr5:53449782-53449783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:53449391..53451285-chr5:53605679..53608585,2	K562	blood:
2	chr5:53441896..53444875-chr5:53446672..53450274,3	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1345815	0.85[CHB][hapmap]
rs151806	0.81[AMR][1000 genomes]
rs154020	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs154041	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs156825	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs156827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs156830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs157069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157072	0.98[ASN][1000 genomes]
rs157073	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1644818	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs165942	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16882414	0.85[CHB][hapmap]
rs16882451	0.85[CHB][hapmap]
rs202168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2547538	1.00[CHB][hapmap]
rs25853	0.82[ASN][1000 genomes]
rs26608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs26609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26610	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs26775	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26776	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277320	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277321	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277323	0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277326	0.82[AMR][1000 genomes]
rs277327	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277328	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277329	0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27776	0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs278065	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279743	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs279744	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs28033	1.00[CHB][hapmap]
rs35006	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs35545340	0.83[ASN][1000 genomes]
rs3797254	0.85[CHB][hapmap]
rs3797255	0.85[CHB][hapmap]
rs3843452	0.93[CHB][hapmap]
rs464888	0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs4865808	0.93[CHB][hapmap]
rs4865809	0.93[CHB][hapmap]
rs586405	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs682103	1.00[CHB][hapmap]
rs6866862	0.92[CHB][hapmap]
rs700911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs700915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1015340	chr5:53326385-53471882	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
19	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
20	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
21	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53409200-53465600	Weak transcription	Fetal Intestine Large	intestine
2	chr5:53425400-53467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:53428000-53471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:53429400-53455800	Weak transcription	Fetal Intestine Small	intestine
5	chr5:53431800-53474000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:53432000-53462400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:53432200-53467600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:53432600-53462000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr5:53433000-53480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:53435000-53462000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:53441800-53461600	Weak transcription	Primary B cells from cord blood	blood
12	chr5:53441800-53461800	Weak transcription	Primary T cells from cord blood	blood
13	chr5:53442400-53464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:53442800-53468400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:53443000-53461600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:53443000-53466000	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:53443200-53473800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:53443600-53462200	Weak transcription	Ovary	ovary
19	chr5:53443600-53473800	Weak transcription	Left Ventricle	heart
20	chr5:53443800-53468600	Weak transcription	Adipose Nuclei	Adipose
21	chr5:53444000-53472800	Weak transcription	Lung	lung
22	chr5:53444400-53455000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:53445200-53457800	Weak transcription	Small Intestine	intestine
24	chr5:53445200-53466000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr5:53445600-53452800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:53445800-53455400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:53445800-53455600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:53445800-53468000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:53447000-53452000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:53447200-53452000	Weak transcription	K562	blood
31	chr5:53448200-53461600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:53448600-53455400	Weak transcription	Fetal Heart	heart
33	chr5:53448800-53461200	Weak transcription	Liver	Liver
34	chr5:53448800-53465600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links