Variant report

Variant	rs35364051
Chromosome Location	chr20:25655264-25655265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25655195-25655380	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr20:25655117-25655755	GM12878	blood:	n/a	n/a
3	POLR2A	chr20:25655140-25655695	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:25655181-25655562	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr20:25655021-25655523	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:25655062-25655701	HepG2	liver:	n/a	n/a
7	POLR2A	chr20:25654971-25657550	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr20:25654914-25655692	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr20:25655234-25655782	PFSK-1	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25603937..25605836-chr20:25653672..25656998,3	MCF-7	breast:
2	chr20:25652247..25655467-chr20:25656048..25658706,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-1	chr20:25654488-25658710	ENSG00000213742.2

No data

Variant related genes	Relation type
MED28P7	TF binding region
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11699872	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12480853	0.84[JPT][hapmap]
rs2072977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs35016365	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35672749	0.81[ASN][1000 genomes]
rs59046052	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6050690	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6050790	0.89[CHB][hapmap]
rs6115218	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6115241	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6132842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs6132851	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6132857	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132858	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132861	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6132862	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6132863	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6132864	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6138595	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138604	0.93[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6138611	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6138622	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138623	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138625	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138631	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138633	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138643	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138647	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138650	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6138651	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6138653	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs878176	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs35364051	NINL	cis	cerebellum	SCAN
rs35364051	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs35364051	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs35364051	PYGB	cis	Whole Blood	GTEx
rs35364051	ABHD12	cis	lymphoblastoid	seeQTL
rs35364051	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs35364051	NINL	cis	parietal	SCAN
rs35364051	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25650600-25655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:25650600-25657000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:25651600-25659600	Strong transcription	Fetal Brain Female	brain
4	chr20:25651800-25655400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr20:25652000-25655600	Weak transcription	Fetal Heart	heart
6	chr20:25652000-25659600	Strong transcription	Brain Germinal Matrix	brain
7	chr20:25652600-25658800	Strong transcription	Fetal Stomach	stomach
8	chr20:25653000-25657000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:25653000-25663600	Strong transcription	HSMM	muscle
10	chr20:25653200-25655800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr20:25653200-25656800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:25653200-25657400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr20:25653200-25657400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:25653200-25659600	Strong transcription	Fetal Intestine Small	intestine
15	chr20:25653200-25662800	Strong transcription	Fetal Lung	lung
16	chr20:25653400-25656800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr20:25653400-25656800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr20:25653400-25656800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:25653400-25656800	Strong transcription	NH-A	brain
20	chr20:25653400-25657000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:25653400-25657400	Strong transcription	A549	lung
22	chr20:25653400-25657600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr20:25653400-25657600	Strong transcription	Brain Substantia Nigra	brain
24	chr20:25653400-25657800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr20:25653400-25658200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr20:25653400-25658600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr20:25653400-25658800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr20:25653400-25659200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr20:25653400-25659400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:25653400-25659600	Strong transcription	Brain Angular Gyrus	brain
31	chr20:25653400-25659600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr20:25653400-25659600	Strong transcription	Ovary	ovary
33	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr20:25653400-25659600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr20:25653400-25661000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr20:25653400-25662400	Strong transcription	Liver	Liver
37	chr20:25653400-25663600	Strong transcription	Dnd41	blood
38	chr20:25653400-25664200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr20:25653600-25655400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:25653600-25655600	Strong transcription	Adipose Nuclei	Adipose
41	chr20:25653600-25656600	Strong transcription	Brain Anterior Caudate	brain
42	chr20:25653600-25656800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr20:25653600-25657000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:25653600-25657000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr20:25653600-25657000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr20:25653600-25657000	Strong transcription	HMEC	breast
47	chr20:25653600-25657000	Strong transcription	NHDF-Ad	bronchial
48	chr20:25653600-25657000	Strong transcription	NHEK	skin
49	chr20:25653600-25657400	Strong transcription	Pancreas	Pancrea
50	chr20:25653600-25657600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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