Variant report

Variant	rs60288484
Chromosome Location	chr3:135916678-135916679
allele	A/T
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	POLR2A	chr3:135913253-135916718	Hela-S3	cervix:	n/a	n/a
2	GATA1	chr3:135913718-135916708	PBDE	blood:	n/a	chr3:135916401-135916417 chr3:135916405-135916412 chr3:135916404-135916414 chr3:135916402-135916412 chr3:135916398-135916419 chr3:135916405-135916412 chr3:135916405-135916412
3	POLR2A	chr3:135913666-135916815	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF384	chr3:135915174-135917085	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:135913750-135916687	PANC-1	pancreas:	n/a	n/a
6	MYC	chr3:135914220-135916840	K562	blood:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
7	MXI1	chr3:135911459-135916721	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:135913427-135916793	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:135913162-135916702	GM12878	blood:	n/a	n/a
10	HCFC1	chr3:135913951-135916889	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:135913137-135917144	PBDE	blood:	n/a	n/a
12	POLR2A	chr3:135914267-135916731	HepG2	liver:	n/a	n/a
13	BRCA1	chr3:135914880-135916809	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:135913864-135916829	IMR90	lung:	n/a	n/a
15	MYC	chr3:135915043-135916756	MCF10A-Er-Src	breast:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
16	POLR2A	chr3:135916199-135916693	PFSK-1	brain:	n/a	n/a
17	RFX5	chr3:135913625-135916730	Hela-S3	cervix:	n/a	chr3:135913677-135913685
18	MBD4	chr3:135914948-135916752	HepG2	liver:	n/a	n/a
19	MAX	chr3:135912734-135916694	NB4	blood:	n/a	chr3:135915503-135915512 chr3:135915503-135915513 chr3:135915501-135915510 chr3:135915504-135915511 chr3:135915499-135915514 chr3:135915734-135915744
20	FOXA1	chr3:135915167-135916761	HepG2	liver:	n/a	chr3:135916520-135916535 chr3:135916303-135916315
21	POLR2A	chr3:135913300-135917197	HepG2	liver:	n/a	n/a
22	ZNF384	chr3:135913125-135916803	K562	blood:	n/a	n/a
23	TBP	chr3:135914109-135916947	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:135913275-135916716	GM18951	blood:	n/a	n/a
25	FOXA1	chr3:135916107-135916734	HepG2	liver:	n/a	chr3:135916520-135916535 chr3:135916303-135916315
26	ZNF274	chr3:135916255-135917083	K562	blood:	n/a	n/a
27	POLR2A	chr3:135914170-135917278	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:135913308..135916970-chr3:135973705..135976198,3	K562	blood:
2	chr3:135913275..135917052-chr3:135966241..135970685,15	MCF-7	breast:
3	chr3:135912206..135917353-chr3:135967047..135972220,20	MCF-7	breast:
4	chr3:135871720..135874662-chr3:135916367..135919284,3	MCF-7	breast:
5	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
6	chr3:135915695..135917970-chr3:135924534..135927537,3	K562	blood:
7	chr3:135916249..135918777-chr3:135964014..135966844,3	K562	blood:
8	chr3:135912902..135916874-chr3:136469598..136473232,8	MCF-7	breast:
9	chr3:135912817..135916962-chr3:136469681..136473212,8	K562	blood:
10	chr3:135915450..135917077-chr3:136578286..136581089,2	MCF-7	breast:
11	chr3:135914663..135917728-chr3:135920669..135925255,5	MCF-7	breast:
12	chr3:135914989..135917015-chr3:136470237..136472481,3	K562	blood:
13	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:

Variant related genes	Relation type
MSL2	TF binding region
ENSG00000241438	Chromatin interaction
ENSG00000244740	Chromatin interaction
ENSG00000158092	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000114054	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10935178	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3872588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59747718	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60149787	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771887	1.00[ASN][1000 genomes]
rs6781817	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800570	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619852	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634492	1.00[ASN][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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60288484	IL20RB	cis	Artery Tibial	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135910800-135916800	Active TSS	K562	blood
2	chr3:135912200-135916800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:135914400-135916800	Active TSS	HepG2	liver
4	chr3:135915200-135917000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:135915400-135916800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:135915400-135917400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr3:135915600-135916800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:135915600-135917200	Flanking Active TSS	Dnd41	blood
9	chr3:135915800-135916800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:135916000-135916800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:135916000-135916800	Flanking Active TSS	Fetal Heart	heart
12	chr3:135916000-135916800	Flanking Active TSS	GM12878-XiMat	blood
13	chr3:135916000-135916800	Flanking Active TSS	NHEK	skin
14	chr3:135916200-135916800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:135916200-135916800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:135916200-135916800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:135916200-135916800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr3:135916200-135916800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr3:135916200-135916800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr3:135916200-135916800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr3:135916200-135916800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr3:135916200-135916800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr3:135916200-135916800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:135916200-135916800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:135916200-135917200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:135916200-135917200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:135916200-135917200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:135916200-135917400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:135916200-135922600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:135916400-135916800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:135916400-135916800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:135916400-135916800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:135916400-135916800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr3:135916400-135917000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr3:135916400-135917000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:135916400-135917200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:135916400-135917200	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:135916400-135917200	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:135916400-135917200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:135916400-135917200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:135916400-135917400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:135916400-135917400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:135916400-135917400	Enhancers	Colon Smooth Muscle	Colon
44	chr3:135916600-135916800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:135916600-135916800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr3:135916600-135916800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:135916600-135916800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:135916600-135916800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:135916600-135916800	Enhancers	Brain Cingulate Gyrus	brain
50	chr3:135916600-135916800	Enhancers	Colonic Mucosa	Colon

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