Variant report

Variant	rs12633538
Chromosome Location	chr3:55918848-55918849
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12108171	0.83[EUR][1000 genomes]
rs12636793	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1379710	0.81[ASN][1000 genomes]
rs1458066	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17056061	0.87[AMR][1000 genomes]
rs17056081	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17056090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17056093	0.82[AMR][1000 genomes]
rs17056098	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1902861	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35046325	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55675302	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55682897	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55724092	0.83[EUR][1000 genomes]
rs55967115	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55971093	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56211981	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62253660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62253661	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62253664	0.83[EUR][1000 genomes]
rs62253666	0.83[EUR][1000 genomes]
rs62253667	0.83[EUR][1000 genomes]
rs62253670	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62255832	0.87[AMR][1000 genomes]
rs62255835	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62256771	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256772	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256773	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256774	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256778	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6763408	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6766607	0.87[AMR][1000 genomes]
rs6769408	0.87[AMR][1000 genomes]
rs73073394	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73075332	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73075334	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs733509	0.83[AMR][1000 genomes]
rs7609626	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7617166	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs7618265	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7636943	0.87[CEU][hapmap]
rs7639013	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7649504	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs897965	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs993594	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv876815	chr3:55895409-55979964	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55893600-55923600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:55903800-55922000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:55913400-55919400	Weak transcription	Fetal Kidney	kidney
4	chr3:55914200-55919200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:55914600-55919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:55914600-55919000	Weak transcription	NHLF	lung
7	chr3:55914800-55919200	Weak transcription	Fetal Lung	lung
8	chr3:55915400-55925800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:55916400-55919400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:55916400-55921800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:55916400-55922200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:55916800-55919200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:55916800-55919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:55916800-55919200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:55916800-55919400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:55916800-55919600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:55917000-55922000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:55917600-55919400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:55918000-55919200	Enhancers	NHEK	skin
20	chr3:55918000-55920200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr3:55918000-55921600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:55918400-55920000	Enhancers	Hela-S3	cervix
23	chr3:55918400-55921200	Enhancers	HMEC	breast
24	chr3:55918600-55919600	Enhancers	Placenta	Placenta
25	chr3:55918600-55920000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:55918600-55920200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:55918600-55921000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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