Variant report

Variant	rs1978376
Chromosome Location	chr2:56542739-56542740
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:56542595..56543142-chr4:88834329..88835129,2	MCF-7	breast:
2	chr2:56535064..56538835-chr2:56538969..56542795,4	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10173561	0.86[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs10178971	0.82[CHB][hapmap]
rs10179998	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10183017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10198922	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10200099	0.82[ASN][1000 genomes]
rs10202401	0.81[ASN][1000 genomes]
rs10206915	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10460558	0.95[JPT][hapmap]
rs12469239	0.83[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1978377	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1990759	0.83[ASN][1000 genomes]
rs2058870	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2058871	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2111470	0.95[JPT][hapmap]
rs2111472	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2216329	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2869809	0.83[CHB][hapmap]
rs3886957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141565	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4141566	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57973944	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6706818	0.95[JPT][hapmap]
rs6710324	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6721952	0.83[ASN][1000 genomes]
rs6722198	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6731831	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6761258	0.89[EUR][1000 genomes]
rs7601878	0.83[ASN][1000 genomes]
rs9679639	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9808260	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][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	nsv530516	chr2:56447922-56633505	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv522006	chr2:56496589-56545845	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv874170	chr2:56496589-56590865	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv834093	chr2:56538097-56708677	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1004449	chr2:56538460-56715861	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56527400-56547400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:56527600-56561000	Weak transcription	HSMM	muscle
3	chr2:56540400-56543400	Enhancers	Adipose Nuclei	Adipose
4	chr2:56541200-56542800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:56541400-56545400	Weak transcription	Left Ventricle	heart
6	chr2:56541600-56543400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:56542400-56542800	Weak transcription	Psoas Muscle	Psoas
8	chr2:56542600-56543400	Enhancers	Fetal Muscle Leg	muscle

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