Variant report

Variant	rs6115210
Chromosome Location	chr20:25545249-25545250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13040726	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1983974	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387976	0.90[AFR][1000 genomes]
rs34485039	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs374701	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752273	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs376742	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390123	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400357	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404775	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405822	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409853	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422148	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4423675	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs443009	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815429	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815431	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815437	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6037158	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050679	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076343	1.00[ASN][1000 genomes]
rs6076358	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076364	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6076366	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6076369	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6083845	1.00[ASN][1000 genomes]
rs6083851	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083860	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083891	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6107060	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6115188	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132845	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138593	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869358	1.00[ASN][1000 genomes]
rs958075	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
18	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6115210	NINL	cis	Thyroid	GTEx
rs6115210	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6115210	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6115210	PYGB	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
3	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:25531000-25554000	Weak transcription	Osteobl	bone
5	chr20:25531200-25559600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:25532600-25551600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr20:25532600-25559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:25532600-25565000	Weak transcription	HSMMtube	muscle
9	chr20:25533400-25546000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr20:25533400-25549600	Weak transcription	Fetal Intestine Small	intestine
11	chr20:25534800-25550000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:25534800-25551800	Weak transcription	HUVEC	blood vessel
13	chr20:25534800-25557600	Weak transcription	Pancreas	Pancrea
14	chr20:25534800-25561400	Weak transcription	Right Atrium	heart
15	chr20:25535000-25545400	Weak transcription	Thymus	Thymus
16	chr20:25535000-25546400	Weak transcription	Ovary	ovary
17	chr20:25535000-25550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:25535000-25550200	Weak transcription	Gastric	stomach
19	chr20:25535000-25554400	Weak transcription	Brain Anterior Caudate	brain
20	chr20:25535000-25560000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:25535000-25561400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr20:25535200-25546000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr20:25535800-25565000	Weak transcription	Fetal Kidney	kidney
24	chr20:25540400-25545600	Weak transcription	Fetal Heart	heart
25	chr20:25540800-25549400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr20:25540800-25552600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:25541200-25549400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr20:25541200-25550000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr20:25541600-25546200	Weak transcription	A549	lung
30	chr20:25541800-25546400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:25544200-25546200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr20:25544600-25545600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr20:25544600-25554000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr20:25544600-25565000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr20:25544800-25545600	Weak transcription	HepG2	liver
36	chr20:25544800-25546000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr20:25544800-25546000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr20:25544800-25546000	Weak transcription	Fetal Lung	lung
39	chr20:25544800-25546400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr20:25544800-25549000	Weak transcription	Brain Germinal Matrix	brain
41	chr20:25544800-25550000	Weak transcription	Dnd41	blood
42	chr20:25544800-25551200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr20:25544800-25554400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr20:25544800-25559600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr20:25545000-25549800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr20:25545200-25549000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25545200-25549200	Weak transcription	Fetal Stomach	stomach

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