Variant report

Variant	rs2297982
Chromosome Location	chr6:54172959-54172960
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	RELA	chr6:54172203-54173624	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
TINAG	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]
rs10085239	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10484646	0.83[EUR][1000 genomes]
rs12204972	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12213363	0.86[ASN][1000 genomes]
rs16885209	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2136134	0.86[ASN][1000 genomes]
rs2202801	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2211241	0.90[ASN][1000 genomes]
rs2297985	0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3777650	0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3777656	0.84[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs3777658	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777659	0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3777660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822896	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs3822897	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs57447968	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58128009	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59348077	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60267994	0.86[ASN][1000 genomes]
rs61106945	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296750	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs9464051	0.92[ASN][1000 genomes]
rs9464052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474797	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54168800-54176400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:54171800-54173800	Enhancers	HepG2	liver
3	chr6:54171800-54176600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:54172200-54176200	Active TSS	Fetal Kidney	kidney
5	chr6:54172400-54176600	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:54172600-54173000	Flanking Active TSS	Fetal Intestine Small	intestine
7	chr6:54172600-54175200	Active TSS	Rectal Smooth Muscle	rectum
8	chr6:54172600-54176200	Active TSS	Colonic Mucosa	Colon
9	chr6:54172800-54173000	Flanking Active TSS	Fetal Intestine Large	intestine
10	chr6:54172800-54173600	Enhancers	A549	lung
11	chr6:54172800-54176600	Active TSS	Rectal Mucosa Donor 31	rectum

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