Variant report

Variant	rs11729535
Chromosome Location	chr4:55198205-55198206
allele	A/G
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	POLR2A	chr4:55197981-55198241	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000248184	TF binding region

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10016845	0.81[ASN][1000 genomes]
rs10028483	0.86[ASN][1000 genomes]
rs10029431	0.87[ASN][1000 genomes]
rs11726309	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11728929	0.89[ASN][1000 genomes]
rs11732117	0.85[ASN][1000 genomes]
rs11732388	0.91[ASN][1000 genomes]
rs11737169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499807	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1574493	0.83[AMR][1000 genomes]
rs17084148	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17084178	0.81[ASN][1000 genomes]
rs1873774	0.82[ASN][1000 genomes]
rs1873775	0.82[ASN][1000 genomes]
rs1873776	0.82[ASN][1000 genomes]
rs2087806	0.86[ASN][1000 genomes]
rs28379127	0.88[ASN][1000 genomes]
rs28714526	0.85[ASN][1000 genomes]
rs4583821	0.89[ASN][1000 genomes]
rs4864510	0.86[ASN][1000 genomes]
rs4864879	0.88[ASN][1000 genomes]
rs4864880	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4864881	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56342025	0.89[ASN][1000 genomes]
rs57765231	0.88[ASN][1000 genomes]
rs62299414	0.89[ASN][1000 genomes]
rs62299416	0.85[ASN][1000 genomes]
rs62299418	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6850695	0.85[ASN][1000 genomes]
rs73234205	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991681	0.86[ASN][1000 genomes]
rs9994113	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv4341	chr4:55172085-55217655	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55189800-55198800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr4:55197800-55200000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:55197800-55200200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:55198200-55199000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:55198200-55199200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:55198200-55199800	Enhancers	Brain Angular Gyrus	brain
7	chr4:55198200-55199800	Enhancers	Brain Substantia Nigra	brain
8	chr4:55198200-55200200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:55198200-55200800	Enhancers	Brain Hippocampus Middle	brain

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