Variant report

Variant	rs2299520
Chromosome Location	chr7:126431159-126431160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:126085913-126088095..7:126429477-126435211	GM12878	blood:

Variant related genes	Relation type
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1008260	0.96[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10215498	0.96[CEU][hapmap]
rs10215590	0.96[CEU][hapmap]
rs10216287	0.96[CEU][hapmap]
rs10216314	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10239010	0.96[CEU][hapmap]
rs10250459	0.96[CEU][hapmap]
rs10252649	0.96[CEU][hapmap]
rs10254445	0.96[CEU][hapmap]
rs10254692	0.96[CEU][hapmap]
rs10257388	0.82[CEU][hapmap]
rs10271146	0.96[CEU][hapmap]
rs10487460	0.96[CEU][hapmap]
rs10954133	0.96[CEU][hapmap]
rs11763603	0.96[CEU][hapmap]
rs11763734	0.96[CEU][hapmap]
rs11765100	0.92[CEU][hapmap]
rs11769459	0.96[CEU][hapmap]
rs11769491	0.96[CEU][hapmap]
rs11770578	0.96[CEU][hapmap]
rs11773772	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12333442	0.96[CEU][hapmap]
rs12333645	0.96[CEU][hapmap]
rs12706746	0.81[ASN][1000 genomes]
rs12706747	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13222700	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13224779	0.96[CEU][hapmap]
rs13225829	0.92[CEU][hapmap]
rs13226065	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13226841	0.96[CEU][hapmap]
rs13236505	0.96[CEU][hapmap]
rs13239613	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13240076	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13240418	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1361988	0.89[ASN][1000 genomes]
rs1361998	0.96[CEU][hapmap]
rs1361999	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1362000	0.93[CEU][hapmap]
rs1362002	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1362004	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1362005	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1419492	0.89[ASN][1000 genomes]
rs1419508	0.96[CEU][hapmap]
rs1557646	0.96[CEU][hapmap]
rs1592370	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17619947	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17620189	0.96[CEU][hapmap]
rs17620525	0.96[CEU][hapmap]
rs17626816	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17627206	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17683174	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17683391	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17693362	0.96[CEU][hapmap]
rs1946109	1.00[CEU][hapmap]
rs1946114	0.96[CEU][hapmap]
rs1946115	0.96[CEU][hapmap]
rs1989849	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1989850	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2023733	0.96[CEU][hapmap]
rs2023734	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2023735	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2106352	0.81[CEU][hapmap]
rs2106600	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2106601	0.96[CEU][hapmap]
rs2157753	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2157977	0.96[CEU][hapmap]
rs2157978	0.96[CEU][hapmap]
rs2157979	0.96[CEU][hapmap]
rs2214159	0.96[CEU][hapmap]
rs2283071	0.96[CEU][hapmap]
rs2283079	0.89[ASN][1000 genomes]
rs2299508	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2299509	0.96[CEU][hapmap]
rs2299510	0.96[CEU][hapmap]
rs2299511	0.96[CEU][hapmap]
rs2299516	1.00[CEU][hapmap]
rs2299517	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2299518	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2299519	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2896376	0.96[CEU][hapmap]
rs34309246	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35351503	0.82[ASN][1000 genomes]
rs35810597	0.89[ASN][1000 genomes]
rs35825148	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4728053	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4728054	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4728055	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4731330	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4731331	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4731332	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467099	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948500	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6951643	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6951771	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6969572	0.96[CEU][hapmap]
rs6976213	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs727903	0.96[CEU][hapmap]
rs7809518	0.82[ASN][1000 genomes]
rs886179	0.96[CEU][hapmap]
rs929211	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs954661	1.00[CEU][hapmap]

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	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv889187	chr7:126219766-126478190	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1032612	chr7:126417533-126456282	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126429200-126431400	Weak transcription	Brain Hippocampus Middle	brain
2	chr7:126429400-126431400	Weak transcription	Brain Substantia Nigra	brain
3	chr7:126429800-126431400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:126430800-126432600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:126430800-126432600	Enhancers	Brain Anterior Caudate	brain
6	chr7:126430800-126433400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr7:126430800-126433800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:126431000-126433600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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