Variant report

Variant	rs11242616
Chromosome Location	chr5:106319863-106319864
allele	C/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	CHD2	chr5:106319848-106320228	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:106319000-106321470	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:106319533-106320498	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:106319511-106319874	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000251027	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10464034	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11242617	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11242618	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11952311	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11954538	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12521220	0.86[AMR][1000 genomes]
rs12521304	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12522964	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12652005	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12653761	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656884	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12658333	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13152891	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13156523	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13157194	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13162085	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13162783	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170737	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13171064	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13173576	0.82[EUR][1000 genomes]
rs13177006	0.89[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13181242	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13187634	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34025237	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34251658	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34770059	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34813715	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212391	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35418541	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35483020	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35900849	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4264928	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4357022	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4395620	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4409072	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4464676	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58378716	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58703126	0.81[ASN][1000 genomes]
rs62377274	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62377280	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62377285	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62378961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62378962	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62378963	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62378965	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7712577	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7737321	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9986310	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016354	chr5:105752391-106392762	ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv830439	chr5:106192038-106383828	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv882679	chr5:106263197-106399718	Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1841017	chr5:106299280-106325865	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
6	esv1795812	chr5:106308008-106326299	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv1799346	chr5:106308008-106326299	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
8	esv1815884	chr5:106308008-106326299	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
9	esv1843510	chr5:106308008-106326299	Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
10	esv1850520	chr5:106308008-106326299	Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
11	esv1815273	chr5:106308008-106326475	Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv1799129	chr5:106311248-106326299	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv1802235	chr5:106311248-106326299	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
14	esv1817753	chr5:106311248-106326299	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
15	esv1844969	chr5:106311248-106326299	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106313800-106320000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:106314200-106320200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr5:106314400-106320800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:106316000-106322200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:106318200-106320800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:106319200-106320000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:106319600-106321200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
8	chr5:106319800-106320600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
9	chr5:106319800-106321200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
10	chr5:106319800-106321200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
11	chr5:106319800-106321200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr5:106319800-106321400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
13	chr5:106319800-106322000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell

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