Variant report

Variant	rs2786116
Chromosome Location	chr1:197333779-197333780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197324727..197326366-chr1:197333265..197336243,2	K562	blood:
2	chr1:197333298..197333798-chr7:158989503..158990071,2	NB4	blood:
3	chr1:197331402..197332938-chr1:197333106..197334632,2	MCF-7	breast:
4	chr1:197328736..197331087-chr1:197333586..197336442,2	K562	blood:

Variant related genes	Relation type
ENSG00000134376	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10801603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10922234	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs12126335	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs12134409	0.95[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12563307	0.86[CEU][hapmap]
rs1337167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1337168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17554990	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17618358	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2476019	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs2476021	0.82[EUR][1000 genomes]
rs2476023	0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2494269	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2759656	0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2759659	0.81[EUR][1000 genomes]
rs2759661	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2786098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2786100	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2786101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2786103	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2786117	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2786119	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2821101	0.81[EUR][1000 genomes]
rs2821107	0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2821115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2821116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2821117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2821132	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs3122635	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122636	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4915231	0.92[ASN][1000 genomes]
rs4915525	0.93[ASN][1000 genomes]
rs4915526	0.93[ASN][1000 genomes]
rs6428397	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs6664399	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685222	0.95[CEU][hapmap];0.85[TSI][hapmap]
rs7551088	0.90[ASN][1000 genomes]
rs949571	0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197324000-197338800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:197324000-197347000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:197329800-197336400	Weak transcription	Ovary	ovary
4	chr1:197329800-197336800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:197329800-197338400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:197329800-197342400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:197333600-197333800	Enhancers	Brain Anterior Caudate	brain

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