Variant report

Variant	rs12187448
Chromosome Location	chr5:58821703-58821704
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	FOS	chr5:58821476-58822136	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr5:58821572-58822246	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr5:58821700-58822155	HUVEC	blood vessel:	n/a	n/a
4	NR3C1	chr5:58821695-58822265	A549	lung:	n/a	n/a
5	TCF12	chr5:58821589-58822251	A549	lung:	n/a	n/a
6	CTCF	chr5:58821600-58821750	HUVEC	blood vessel:	n/a	n/a
7	JUN	chr5:58821672-58822103	HUVEC	blood vessel:	n/a	n/a
8	NR3C1	chr5:58821672-58822284	A549	lung:	n/a	n/a
9	GATA2	chr5:58821618-58822222	HUVEC	blood vessel:	n/a	n/a
10	NR3C1	chr5:58821637-58822292	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58821597..58822483-chr5:58956197..58956887,3	MCF-7	breast:

Variant related genes	Relation type
NDUFB4P2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10514860	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949561	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187079	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17728654	1.00[JPT][hapmap]
rs17740749	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740767	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795596	1.00[JPT][hapmap]
rs17795692	1.00[JPT][hapmap]
rs17796040	1.00[JPT][hapmap]
rs17796824	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797601	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098699	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4326095	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551023	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075449	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56396168	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861969	1.00[JPT][hapmap]
rs72767794	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767801	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72769704	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717821	1.00[JPT][hapmap]
rs7729912	1.00[JPT][hapmap]
rs7737908	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58810000-58823600	Weak transcription	Colon Smooth Muscle	Colon
2	chr5:58814600-58823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58815400-58830400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:58815800-58823600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:58818400-58822400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:58818800-58823800	Weak transcription	Stomach Mucosa	stomach
7	chr5:58819000-58832600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:58820000-58822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:58820000-58831400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:58820200-58822800	Enhancers	Fetal Intestine Large	intestine
11	chr5:58820600-58822200	Enhancers	Duodenum Mucosa	Duodenum
12	chr5:58820600-58822200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr5:58820800-58823000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:58820800-58824600	Weak transcription	Psoas Muscle	Psoas
15	chr5:58821000-58822000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr5:58821000-58822000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:58821000-58822600	Enhancers	Fetal Intestine Small	intestine
18	chr5:58821000-58828600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:58821200-58823000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:58821400-58822000	Enhancers	HepG2	liver
21	chr5:58821400-58822400	Enhancers	Osteobl	bone
22	chr5:58821400-58822600	Enhancers	HSMM	muscle
23	chr5:58821400-58822600	Enhancers	HSMMtube	muscle
24	chr5:58821400-58822600	Enhancers	NH-A	brain
25	chr5:58821400-58822800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:58821400-58823200	Enhancers	HUVEC	blood vessel
27	chr5:58821600-58822400	Genic enhancers	A549	lung
28	chr5:58821600-58823800	Weak transcription	Brain Substantia Nigra	brain

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