Variant report

Variant	rs6138650
Chromosome Location	chr20:25715507-25715508
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-7	chr20:25714900-25715729	NONHSAT079180

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11699872	0.86[JPT][hapmap]
rs12480853	0.84[JPT][hapmap]
rs35016365	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35364051	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59046052	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6050690	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs6115218	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs6115241	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6132842	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6132851	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6132857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6132858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6132861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132863	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132864	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6138595	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138598	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138601	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6138604	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6138611	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6138616	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6138622	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138623	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6138625	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6138631	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138633	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6138639	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6138647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6138651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138653	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6138728	0.81[MEX][hapmap]
rs878176	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS 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
4	nsv525033	chr20:25688001-25730968	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
6	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
7	nsv1062442	chr20:25714010-25754838	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6138650	NINL	cis	cerebellum	SCAN
rs6138650	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6138650	PYGB	cis	Whole Blood	GTEx
rs6138650	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138650	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6138650	FRG1B	cis	parietal	SCAN
rs6138650	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138650	NINL	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25700400-25725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr20:25701200-25720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:25708000-25715800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr20:25708000-25716200	Weak transcription	Thymus	Thymus
5	chr20:25708000-25717200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:25708000-25717600	Weak transcription	Psoas Muscle	Psoas
7	chr20:25708000-25724600	Weak transcription	Brain Substantia Nigra	brain
8	chr20:25708000-25731400	Weak transcription	Esophagus	oesophagus
9	chr20:25711600-25724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:25713400-25720200	Weak transcription	Primary T cells from cord blood	blood
11	chr20:25713400-25731000	Weak transcription	Left Ventricle	heart
12	chr20:25713600-25720200	Weak transcription	HSMM	muscle
13	chr20:25713600-25721800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr20:25714400-25731200	Weak transcription	Pancreas	Pancrea
15	chr20:25714600-25718600	Weak transcription	NHEK	skin
16	chr20:25714800-25715800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:25715400-25715600	ZNF genes & repeats	Aorta	Aorta
18	chr20:25715400-25715600	ZNF genes & repeats	Gastric	stomach

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