Variant report

Variant	rs2341813
Chromosome Location	chr3:99013299-99013300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10511173	0.88[ASN][1000 genomes]
rs1118911	0.89[ASN][1000 genomes]
rs11721251	0.83[ASN][1000 genomes]
rs13061712	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1318850	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1356924	0.81[ASN][1000 genomes]
rs1383839	0.87[EUR][1000 genomes]
rs1383842	0.81[ASN][1000 genomes]
rs1402263	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1402266	0.85[ASN][1000 genomes]
rs1402267	0.83[ASN][1000 genomes]
rs1402268	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1520678	0.83[ASN][1000 genomes]
rs1520692	0.81[ASN][1000 genomes]
rs1520693	0.81[ASN][1000 genomes]
rs1520694	0.81[ASN][1000 genomes]
rs1574857	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1829553	0.81[ASN][1000 genomes]
rs1996654	0.81[ASN][1000 genomes]
rs2128024	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2139702	0.83[ASN][1000 genomes]
rs2170387	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2170388	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2200017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341809	0.81[ASN][1000 genomes]
rs2341812	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2880156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312686	0.81[ASN][1000 genomes]
rs4327425	0.81[ASN][1000 genomes]
rs4426705	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4572803	0.81[ASN][1000 genomes]
rs4572804	0.81[ASN][1000 genomes]
rs59089459	0.90[EUR][1000 genomes]
rs62283771	0.90[EUR][1000 genomes]
rs6440525	0.89[EUR][1000 genomes]
rs6784043	0.81[ASN][1000 genomes]
rs6786590	0.81[ASN][1000 genomes]
rs6800453	0.83[ASN][1000 genomes]
rs71620012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138428	0.90[EUR][1000 genomes]
rs7373550	0.81[ASN][1000 genomes]
rs7374314	0.81[ASN][1000 genomes]
rs7614880	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7628173	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645284	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9289771	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9289774	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs974686	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9823613	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9831801	0.89[ASN][1000 genomes]
rs9860091	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
2	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798220	chr3:98894142-99020463	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1002786	chr3:98944446-99013936	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv818163	chr3:99005053-99015616	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99013000-99013400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:99013000-99013400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:99013000-99013400	Enhancers	HUVEC	blood vessel
4	chr3:99013000-99013400	Enhancers	Osteobl	bone
5	chr3:99013000-99013600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:99013000-99013600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:99013000-99013600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:99013000-99013600	Enhancers	HMEC	breast
9	chr3:99013000-99013600	Enhancers	NHLF	lung
10	chr3:99013000-99013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:99013000-99014000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:99013200-99013400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:99013200-99013400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:99013200-99013400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr3:99013200-99013400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:99013200-99013400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:99013200-99013400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr3:99013200-99013400	Flanking Active TSS	Dnd41	blood
19	chr3:99013200-99013400	Enhancers	NHDF-Ad	bronchial
20	chr3:99013200-99013400	Flanking Active TSS	NHEK	skin
21	chr3:99013200-99013600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:99013200-99013600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:99013200-99013600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:99013200-99013600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:99013200-99013600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:99013200-99013600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:99013200-99013600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr3:99013200-99013600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:99013200-99013600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:99013200-99013600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:99013200-99013600	Enhancers	Fetal Stomach	stomach
32	chr3:99013200-99013600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr3:99013200-99013800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:99013200-99013800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:99013200-99014000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:99013200-99014200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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