Variant report

Variant	rs498497
Chromosome Location	chr5:60456272-60456273
allele	A/T
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	GATA3	chr5:60456156-60456349	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr5:60455764-60460434	K562	blood:	n/a	n/a
3	POLR2A	chr5:60456204-60456697	SK-N-MC	brain:	n/a	n/a
4	MYC	chr5:60456230-60456875	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:60455708-60456397	GM12878	blood:	n/a	n/a
6	MAFF	chr5:60456248-60456692	K562	blood:	n/a	chr5:60456457-60456475

No.	Distal block	Cell Line	Cell type
1	chr5:60438650..60440310-chr5:60455586..60457304,2	MCF-7	breast:
2	chr5:60431315..60433087-chr5:60453432..60456427,3	K562	blood:
3	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
4	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
5	chr5:59994474..59997876-chr5:60455928..60460228,5	K562	blood:

Variant related genes	Relation type
ENSG00000251279	TF binding region
ENSG00000035499	Chromatin interaction
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10044518	1.00[JPT][hapmap]
rs10044575	1.00[JPT][hapmap]
rs12186613	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188621	1.00[JPT][hapmap]
rs12188882	1.00[JPT][hapmap]
rs159373	1.00[CEU][hapmap];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]
rs159379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159540	0.88[ASN][1000 genomes]
rs167190	0.96[EUR][1000 genomes]
rs1841504	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295529	1.00[CEU][hapmap];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]
rs295530	1.00[CEU][hapmap];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]
rs295538	0.88[EUR][1000 genomes]
rs295547	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295548	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295549	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295550	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs295568	1.00[CEU][hapmap];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]
rs295570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295574	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs298625	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298626	1.00[CEU][hapmap];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]
rs298627	1.00[CEU][hapmap];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]
rs298628	1.00[CEU][hapmap];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]
rs298630	1.00[CEU][hapmap];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]
rs298631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256302	1.00[JPT][hapmap]
rs557092	1.00[CEU][hapmap];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]
rs603018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60436000-60457600	Weak transcription	Esophagus	oesophagus
2	chr5:60440400-60457400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:60446600-60457400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:60446800-60456600	Weak transcription	Fetal Stomach	stomach
5	chr5:60447400-60457400	Weak transcription	Ovary	ovary
6	chr5:60449000-60457200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:60450000-60457400	Weak transcription	Right Ventricle	heart
8	chr5:60450400-60457600	Weak transcription	Lung	lung
9	chr5:60450800-60456400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:60451000-60457200	Weak transcription	Thymus	Thymus
11	chr5:60451200-60456600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:60451400-60457000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:60451600-60456400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:60451800-60457600	Weak transcription	Spleen	Spleen
15	chr5:60452000-60456600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:60452000-60457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:60452400-60456400	Strong transcription	HSMM	muscle
18	chr5:60452600-60456400	Strong transcription	Liver	Liver
19	chr5:60452600-60456400	Weak transcription	Fetal Intestine Small	intestine
20	chr5:60452600-60456800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:60452600-60457000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:60452600-60457600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:60452800-60456400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr5:60453200-60457600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:60453400-60456400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:60453400-60456600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:60453400-60456800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:60453400-60456800	Strong transcription	Fetal Thymus	thymus
29	chr5:60453400-60457400	Weak transcription	Aorta	Aorta
30	chr5:60453600-60456800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr5:60453600-60456800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:60453600-60457400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr5:60453800-60456400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:60453800-60456400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:60453800-60457000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:60453800-60457600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr5:60454000-60456400	Strong transcription	Osteobl	bone
38	chr5:60454000-60457400	Weak transcription	Colonic Mucosa	Colon
39	chr5:60454200-60456400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:60454200-60456600	Weak transcription	Stomach Mucosa	stomach
41	chr5:60454200-60457200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:60454400-60456400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:60454600-60456400	Genic enhancers	Hela-S3	cervix
44	chr5:60454600-60456600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:60454600-60456600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:60454600-60456600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:60454600-60456600	Genic enhancers	HUVEC	blood vessel
48	chr5:60454600-60456800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr5:60454800-60456600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr5:60454800-60456600	Strong transcription	Placenta	Placenta

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