Variant report

Variant	rs6132842
Chromosome Location	chr20:25527069-25527070
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25521309..25522938-chr20:25526944..25528978,2	MCF-7	breast:
2	chr20:25524006..25525778-chr20:25527051..25529614,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11699872	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12480853	0.84[JPT][hapmap]
rs2072975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs2072977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2235605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2235606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2235607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2263205	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2294583	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2482934	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2500403	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs35364051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs59046052	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050690	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6050790	0.89[CHB][hapmap]
rs6115218	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6115241	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6132851	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6132861	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6132863	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6138569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs6138573	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6138576	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6138580	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6138584	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6138595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6138599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6138601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138604	0.93[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6138611	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6138622	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6138623	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6138625	0.97[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6138631	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6138633	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6138639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs723774	0.82[AMR][1000 genomes]
rs878176	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6132842	PYGB	Cis_1M	lymphoblastoid	RTeQTL
rs6132842	PYGB	cis	Whole Blood	GTEx
rs6132842	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs6132842	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6132842	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:25518800-25530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr20:25520000-25532000	Weak transcription	Dnd41	blood
5	chr20:25520200-25529000	Weak transcription	Stomach Mucosa	stomach
6	chr20:25520600-25527400	Weak transcription	Lung	lung
7	chr20:25520600-25528800	Weak transcription	Gastric	stomach
8	chr20:25521000-25530200	Weak transcription	Brain Germinal Matrix	brain
9	chr20:25521200-25529200	Weak transcription	Placenta	Placenta
10	chr20:25521200-25530600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr20:25521400-25529200	Weak transcription	Ovary	ovary
12	chr20:25521400-25530000	Weak transcription	HSMM	muscle
13	chr20:25521400-25532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:25521400-25534200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr20:25521600-25530200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
17	chr20:25522000-25530000	Weak transcription	Colon Smooth Muscle	Colon
18	chr20:25522800-25528800	Weak transcription	Spleen	Spleen
19	chr20:25523000-25527400	Weak transcription	Pancreas	Pancrea
20	chr20:25523000-25529000	Weak transcription	Fetal Intestine Large	intestine
21	chr20:25523000-25529000	Weak transcription	Thymus	Thymus
22	chr20:25523000-25529800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr20:25523800-25528200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr20:25524000-25527200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:25524000-25527600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr20:25524000-25529200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:25524400-25528600	Weak transcription	Esophagus	oesophagus
28	chr20:25524400-25530000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr20:25524600-25529800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:25524600-25529800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr20:25524600-25530000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr20:25524600-25530000	Enhancers	A549	lung
34	chr20:25524800-25527600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr20:25524800-25531600	Enhancers	Fetal Lung	lung
36	chr20:25525000-25527600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr20:25525000-25527800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr20:25525000-25528000	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr20:25525000-25528400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr20:25525000-25529800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr20:25525000-25535400	Enhancers	Fetal Heart	heart
42	chr20:25525200-25527200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr20:25525200-25527400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr20:25525200-25527400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr20:25525200-25527600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr20:25525400-25528600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr20:25525800-25528600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr20:25525800-25530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr20:25525800-25530000	Weak transcription	Osteobl	bone
50	chr20:25526000-25527200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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