Variant report

Variant	rs399529
Chromosome Location	chr1:76595451-76595452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs158620	0.82[EUR][1000 genomes]
rs167050	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172334	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs190861	0.81[EUR][1000 genomes]
rs289676	0.81[EUR][1000 genomes]
rs289698	0.91[ASN][1000 genomes]
rs289699	0.91[ASN][1000 genomes]
rs289700	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289701	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291059	0.80[EUR][1000 genomes]
rs2992503	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011994	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011995	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384233	0.88[EUR][1000 genomes]
rs403449	0.88[EUR][1000 genomes]
rs409245	0.88[EUR][1000 genomes]
rs447383	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs491409	0.85[EUR][1000 genomes]
rs551954	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs552890	0.84[EUR][1000 genomes]
rs61558985	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs622212	0.91[ASN][1000 genomes]
rs643289	0.91[ASN][1000 genomes]
rs915402	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915403	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915404	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv522056	chr1:76573614-76598209	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1488	chr1:76587622-76632635	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv947432	chr1:76591253-76601907	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:76575400-76606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:76576600-76620000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76581800-76596200	Weak transcription	Fetal Intestine Large	intestine
5	chr1:76587800-76602800	Weak transcription	Right Atrium	heart
6	chr1:76588200-76615600	Weak transcription	Left Ventricle	heart
7	chr1:76590200-76595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:76591200-76607800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:76591800-76601400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:76592000-76601400	Weak transcription	Brain Anterior Caudate	brain
11	chr1:76592600-76610800	Weak transcription	Fetal Kidney	kidney
12	chr1:76592800-76605800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:76593000-76601200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:76593000-76608200	Weak transcription	Fetal Lung	lung
15	chr1:76593200-76595600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:76593400-76596800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:76593400-76598600	Strong transcription	Fetal Stomach	stomach
18	chr1:76594000-76601200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:76594000-76601600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:76594200-76601400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:76594200-76601400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:76594200-76607400	Weak transcription	Fetal Brain Female	brain
23	chr1:76594400-76598200	Weak transcription	Aorta	Aorta
24	chr1:76594600-76615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:76595200-76595600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:76595200-76596200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:76595200-76597000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:76595400-76595600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:76595400-76595600	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr1:76595400-76595600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
31	chr1:76595400-76596000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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