Variant report

Variant	rs7540339
Chromosome Location	chr1:171569719-171569720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs56737295	1.00[EUR][1000 genomes]
rs57057228	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57152399	1.00[EUR][1000 genomes]
rs57268639	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57295197	1.00[EUR][1000 genomes]
rs57732262	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58804054	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58832725	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59025168	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59135694	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59660141	1.00[EUR][1000 genomes]
rs59876822	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59907184	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60166114	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61149631	1.00[EUR][1000 genomes]
rs61416201	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73038320	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73038352	1.00[EUR][1000 genomes]
rs73038391	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73038398	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73040395	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534198	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171558800-171573200	Weak transcription	Small Intestine	intestine
2	chr1:171561200-171569800	Weak transcription	Pancreas	Pancrea
3	chr1:171561600-171570000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:171561600-171572200	Weak transcription	Aorta	Aorta
5	chr1:171561800-171570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:171561800-171570200	Weak transcription	Lung	lung
7	chr1:171561800-171570400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:171561800-171572200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:171561800-171576600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:171562000-171572000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:171562200-171571800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:171562200-171575600	Weak transcription	HepG2	liver
13	chr1:171562800-171572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:171562800-171572200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:171563200-171572000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:171564000-171572200	Weak transcription	Fetal Kidney	kidney
17	chr1:171564400-171570600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:171564400-171572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:171564400-171573000	Weak transcription	Adipose Nuclei	Adipose
20	chr1:171564800-171570200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:171566200-171572000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:171569200-171576400	Weak transcription	GM12878-XiMat	blood
23	chr1:171569400-171570200	Enhancers	Liver	Liver
24	chr1:171569600-171570200	Weak transcription	Brain Anterior Caudate	brain

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