Variant report

Variant	rs12074249
Chromosome Location	chr1:98410228-98410229
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	GATA2	chr1:98410080-98410747	HUVEC	blood vessel:	n/a	chr1:98410368-98410382
2	GATA3	chr1:98409808-98410589	SK-N-SH	brain:	n/a	chr1:98409942-98409958
3	EP300	chr1:98408606-98410508	SK-N-SH	brain:	n/a	chr1:98408731-98408745
4	POLR2A	chr1:98410136-98410418	ProgFib	skin:	n/a	n/a
5	YY1	chr1:98410053-98410548	SK-N-SH	brain:	n/a	chr1:98410291-98410313 chr1:98410292-98410300 chr1:98410291-98410301
6	POLR2A	chr1:98410115-98410451	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:98404225..98407168-chr1:98409005..98411442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269998	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10518643	1.00[GIH][hapmap]
rs12081900	1.00[AMR][1000 genomes]
rs12094781	1.00[AMR][1000 genomes]
rs1333721	1.00[GIH][hapmap]
rs13376217	1.00[GIH][hapmap]
rs17117167	1.00[GIH][hapmap]
rs17117175	1.00[GIH][hapmap]
rs17117194	1.00[GIH][hapmap]
rs17117198	1.00[GIH][hapmap]
rs17117203	1.00[GIH][hapmap]
rs17117207	1.00[GIH][hapmap]
rs17117214	1.00[GIH][hapmap]
rs17117218	1.00[GIH][hapmap]
rs17117222	1.00[GIH][hapmap]
rs17117228	1.00[GIH][hapmap]
rs17117234	1.00[GIH][hapmap]
rs17117251	1.00[GIH][hapmap]
rs1855376	1.00[GIH][hapmap]
rs1889227	1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs59356371	1.00[EUR][1000 genomes]
rs61211497	1.00[EUR][1000 genomes]
rs72963706	1.00[EUR][1000 genomes]
rs72979788	1.00[EUR][1000 genomes]
rs72981731	1.00[EUR][1000 genomes]
rs72981733	1.00[EUR][1000 genomes]
rs72981745	1.00[EUR][1000 genomes]
rs72981751	1.00[EUR][1000 genomes]
rs72981754	1.00[EUR][1000 genomes]
rs72981756	1.00[EUR][1000 genomes]
rs72981760	1.00[EUR][1000 genomes]
rs72981761	1.00[EUR][1000 genomes]
rs72981763	1.00[EUR][1000 genomes]
rs72981765	1.00[EUR][1000 genomes]
rs72981766	1.00[EUR][1000 genomes]
rs72981768	1.00[EUR][1000 genomes]
rs72981771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72981774	1.00[EUR][1000 genomes]
rs7517110	1.00[EUR][1000 genomes]
rs7545029	1.00[GIH][hapmap]
rs7553077	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 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	chr1:98407400-98410800	Enhancers	HUVEC	blood vessel
2	chr1:98408600-98410400	Enhancers	Dnd41	blood
3	chr1:98409000-98410400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:98409200-98410400	Enhancers	HMEC	breast
5	chr1:98409200-98410800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:98409400-98413200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:98409400-98437800	Weak transcription	HSMM	muscle
8	chr1:98409600-98410400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:98409600-98410800	Enhancers	NHDF-Ad	bronchial
10	chr1:98409600-98410800	Enhancers	Osteobl	bone
11	chr1:98409600-98412600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:98409600-98413400	Weak transcription	NH-A	brain
13	chr1:98409600-98455000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:98410000-98410800	Enhancers	Muscle Satellite Cultured Cells	--

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