Variant report

Variant	rs4408417
Chromosome Location	chr13:39377187-39377188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11618193	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12867320	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1577040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4335664	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4381466	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4587834	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9532282	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9532283	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9548460	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs963798	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39360400-39377600	Weak transcription	Fetal Kidney	kidney
2	chr13:39369800-39379000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:39372400-39377400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:39373800-39377400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr13:39375400-39377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:39375400-39377600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:39376000-39388800	Weak transcription	Gastric	stomach
8	chr13:39376400-39377200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:39376400-39377400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:39376600-39377400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:39376600-39377600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr13:39376600-39379600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr13:39376600-39380600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr13:39376800-39377400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:39376800-39377600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr13:39377000-39379200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr13:39377000-39380000	Enhancers	Cortex derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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