Variant report

Variant	rs17825041
Chromosome Location	chr2:180614165-180614166
allele	C/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	FOS	chr2:180614125-180614336	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr2:180614017-180614421	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr2:180613915-180614373	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr2:180613996-180614400	IMR90	lung:	n/a	chr2:180614006-180614015
5	REST	chr2:180614006-180614395	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr2:180613820-180614577	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr2:180613734-180614612	SK-N-SH	brain:	n/a	chr2:180614440-180614448 chr2:180614144-180614151
8	JUND	chr2:180613909-180614441	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr2:180613936-180614548	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr2:180613920-180614506	SK-N-SH	brain:	n/a	chr2:180614440-180614448 chr2:180614144-180614151
11	GATA3	chr2:180613866-180614560	SK-N-SH	brain:	n/a	chr2:180614380-180614388
12	POLR2A	chr2:180614017-180614418	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr2:180613964-180614403	SK-N-SH_RA	brain:	n/a	chr2:180614006-180614015

Variant related genes	Relation type
ZNF385B	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10930884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930885	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1385970	1.00[CHB][hapmap]
rs1486232	1.00[CHB][hapmap]
rs165383	1.00[CHB][hapmap]
rs16867038	1.00[CHB][hapmap]
rs16867040	1.00[CHB][hapmap]
rs16867042	1.00[CHB][hapmap]
rs17772985	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs17773184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773667	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17773899	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17773927	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17775571	1.00[CHB][hapmap]
rs17775913	1.00[CHB][hapmap]
rs17775991	1.00[CHB][hapmap]
rs17776109	1.00[CHB][hapmap]
rs17823821	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs17823881	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs17824301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs17824564	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17824913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825317	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17825747	1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17831917	1.00[CHB][hapmap]
rs187744	1.00[CHB][hapmap]
rs2126424	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs2367798	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap]
rs2367800	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2630544	0.92[AMR][1000 genomes]
rs56342697	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56837904	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59847923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60243803	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180392	1.00[ASN][1000 genomes]
rs62181524	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62181526	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6433805	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6433806	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6433808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6718670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727665	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap]
rs6738348	1.00[CHB][hapmap]
rs73046887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73046901	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048517	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7557892	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570042	1.00[CHB][hapmap]
rs7574741	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs7581371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602719	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180610800-180621200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180613600-180615600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:180613800-180614200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:180613800-180614400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:180613800-180614400	Enhancers	Fetal Heart	heart
6	chr2:180613800-180614600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:180614000-180614200	Enhancers	Right Atrium	heart
8	chr2:180614000-180614400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:180614000-180614400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:180614000-180614600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:180614000-180614600	Enhancers	HSMM	muscle
12	chr2:180614000-180614600	Enhancers	HSMMtube	muscle
13	chr2:180614000-180614600	Enhancers	NHDF-Ad	bronchial
14	chr2:180614000-180615000	Enhancers	Fetal Lung	lung

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