Variant report

Variant	rs60220475
Chromosome Location	chr3:138316142-138316143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr3:138316126-138316614	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:138313714..138315292-chr3:138315408..138318314,2	K562	blood:
2	chr3:138308891..138310571-chr3:138313902..138316460,2	K562	blood:
3	chr3:138310314..138312413-chr3:138315463..138317379,2	MCF-7	breast:

Variant related genes	Relation type
CEP70	TF binding region
ENSG00000114107	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10428128	1.00[EUR][1000 genomes]
rs11921301	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11923867	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926199	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1824206	0.83[AFR][1000 genomes]
rs1865	1.00[EUR][1000 genomes]
rs57333469	1.00[EUR][1000 genomes]
rs57752939	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57873424	1.00[EUR][1000 genomes]
rs57952208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58205884	1.00[EUR][1000 genomes]
rs58886826	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59086521	1.00[EUR][1000 genomes]
rs59316948	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59336525	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60121038	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60331753	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61361298	1.00[EUR][1000 genomes]
rs6794254	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73864577	1.00[EUR][1000 genomes]
rs73864583	1.00[EUR][1000 genomes]
rs73864584	1.00[EUR][1000 genomes]
rs73864585	1.00[EUR][1000 genomes]
rs7625183	1.00[EUR][1000 genomes]
rs7645632	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138313600-138327200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:138313800-138316200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:138313800-138319000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:138313800-138327200	Weak transcription	Psoas Muscle	Psoas
5	chr3:138314000-138319000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:138314000-138319000	Weak transcription	Osteobl	bone
7	chr3:138314000-138319200	Weak transcription	Adipose Nuclei	Adipose
8	chr3:138314000-138321400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:138314000-138327000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:138314000-138327200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:138314200-138319200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:138314200-138319400	Weak transcription	Stomach Mucosa	stomach
13	chr3:138314200-138327000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:138315000-138316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:138315000-138317000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:138315400-138317200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:138315800-138316400	Enhancers	Pancreas	Pancrea
18	chr3:138315800-138316400	Enhancers	GM12878-XiMat	blood
19	chr3:138316000-138316200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:138316000-138316400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr3:138316000-138317000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr3:138316000-138317200	Enhancers	Liver	Liver
23	chr3:138316000-138317200	Enhancers	HepG2	liver

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