Variant report

Variant	rs6048333
Chromosome Location	chr20:22738814-22738815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22737582..22739507-chr20:22742394..22744607,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11087395	0.83[EUR][1000 genomes]
rs11907108	0.82[EUR][1000 genomes]
rs12479587	0.85[EUR][1000 genomes]
rs13036614	0.82[EUR][1000 genomes]
rs13036740	0.82[EUR][1000 genomes]
rs13037649	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13037911	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs13037976	0.83[EUR][1000 genomes]
rs13038208	0.81[EUR][1000 genomes]
rs13038520	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs13039411	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs13039474	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs13040538	0.81[EUR][1000 genomes]
rs13044931	0.82[EUR][1000 genomes]
rs4371419	0.82[EUR][1000 genomes]
rs4514951	0.82[EUR][1000 genomes]
rs4603850	0.82[EUR][1000 genomes]
rs6036197	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6036200	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036203	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6036204	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6036205	0.82[EUR][1000 genomes]
rs6036206	0.82[EUR][1000 genomes]
rs6036212	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036213	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048291	0.81[EUR][1000 genomes]
rs6048298	0.81[EUR][1000 genomes]
rs6048300	0.87[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs6048302	0.83[TSI][hapmap]
rs6048326	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048327	0.83[EUR][1000 genomes]
rs6048328	0.83[EUR][1000 genomes]
rs6048331	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048332	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6075943	0.82[EUR][1000 genomes]
rs6113789	0.81[EUR][1000 genomes]
rs7262725	0.82[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7270196	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs7270365	0.82[EUR][1000 genomes]
rs7270374	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs965762	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs965763	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6048333	GGTLC1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22726000-22739000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:22734800-22745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:22736600-22739200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:22736600-22741200	Weak transcription	Esophagus	oesophagus
5	chr20:22736600-22741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:22737400-22739000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr20:22737600-22739400	Enhancers	HSMMtube	muscle
8	chr20:22737800-22739600	Enhancers	Aorta	Aorta
9	chr20:22737800-22740000	Enhancers	HSMM	muscle
10	chr20:22737800-22749000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:22738000-22739200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:22738000-22739400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:22738000-22739400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:22738000-22739400	Enhancers	NH-A	brain
15	chr20:22738000-22739600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:22738000-22739600	Enhancers	Fetal Muscle Leg	muscle
17	chr20:22738000-22739600	Enhancers	Placenta	Placenta
18	chr20:22738400-22739400	Enhancers	Dnd41	blood
19	chr20:22738600-22739000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr20:22738600-22739000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr20:22738600-22739200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr20:22738600-22739400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:22738600-22740800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr20:22738600-22743000	Weak transcription	A549	lung
25	chr20:22738800-22739400	Enhancers	Placenta Amnion	Placenta Amnion

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