Variant report

Variant	rs4815438
Chromosome Location	chr20:25606369-25606370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25605696-25607611	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr20:25605863-25606817	PANC-1	pancreas:	n/a	n/a
3	HEY1	chr20:25605730-25606685	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:25605901-25606803	HepG2	liver:	n/a	n/a
5	HEY1	chr20:25605897-25606965	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:25605887-25607858	K562	blood:	n/a	n/a
7	POLR2A	chr20:25603912-25606817	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr20:25603845-25607875	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr20:25605729-25607717	HepG2	liver:	n/a	n/a
10	POLR2A	chr20:25602890-25606578	HepG2	liver:	n/a	n/a
11	POLR2A	chr20:25606142-25606517	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25604862..25606415-chr20:25633775..25635785,2	MCF-7	breast:
2	chr20:25590781..25592605-chr20:25602144..25606440,3	MCF-7	breast:
3	chr20:25564265..25567754-chr20:25602950..25606854,10	MCF-7	breast:
4	chr20:25474956..25477524-chr20:25604184..25606432,2	MCF-7	breast:
5	chr20:25601566..25607773-chr20:25608657..25615631,12	MCF-7	breast:
6	chr20:25604068..25607059-chr20:25675582..25678596,4	MCF-7	breast:
7	chr20:25571499..25573188-chr20:25604906..25607655,2	K562	blood:
8	chr20:25602422..25607796-chr20:25675112..25679388,9	K562	blood:
9	chr20:25604700..25606724-chr20:25650561..25652560,2	MCF-7	breast:
10	chr20:25604858..25606778-chr20:25612734..25614672,2	MCF-7	breast:
11	chr20:25603625..25606406-chr20:25665177..25670447,5	MCF-7	breast:

No data

Variant related genes	Relation type
NANP	TF binding region
ENSG00000101004	Chromatin interaction
ENSG00000251883	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000242236	Chromatin interaction
ENSG00000130684	Chromatin interaction
ENSG00000236542	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11087526	0.92[ASN][1000 genomes]
rs11698953	0.88[ASN][1000 genomes]
rs11698992	0.90[ASN][1000 genomes]
rs11699872	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11700297	0.91[ASN][1000 genomes]
rs11700338	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12480853	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs12481037	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12625991	0.90[ASN][1000 genomes]
rs1343355	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1343357	0.82[ASN][1000 genomes]
rs1546890	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16987966	0.92[ASN][1000 genomes]
rs1888037	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2050097	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2281212	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs3736720	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3764694	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4813576	0.92[ASN][1000 genomes]
rs4815445	0.86[LWK][hapmap];0.80[YRI][hapmap]
rs4815448	0.87[ASN][1000 genomes]
rs57803591	0.98[ASN][1000 genomes]
rs6037190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6050690	0.82[CHB][hapmap]
rs6050791	0.83[ASW][hapmap];0.86[LWK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs6050796	0.83[ASW][hapmap];0.86[LWK][hapmap]
rs6050814	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6050858	0.80[YRI][hapmap]
rs6050867	0.83[ASW][hapmap];0.80[LWK][hapmap]
rs6115202	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs6115227	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6115241	0.87[CHB][hapmap]
rs7260957	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs73597820	0.88[ASN][1000 genomes]
rs73597824	0.87[ASN][1000 genomes]
rs926486	0.88[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4815438	ZNF337	cis	lymphoblastoid	seeQTL
rs4815438	CTD-2514C3.1	cis	Artery Tibial	GTEx
rs4815438	NANP	cis	cerebellum	SCAN
rs4815438	PYGB	cis	multi-tissue	Pritchard
rs4815438	HDHD4	cis	multi-tissue	Pritchard
rs4815438	HSS00124743	cis	multi-tissue	Pritchard
rs4815438	ZNF337	cis	cerebellum	SCAN
rs4815438	C20orf22	cis	multi-tissue	Pritchard
rs4815438	CST3	cis	parietal	SCAN
rs4815438	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25603400-25606600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:25605400-25616800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:25605400-25628600	Weak transcription	Left Ventricle	heart
4	chr20:25605400-25630400	Weak transcription	Aorta	Aorta
5	chr20:25605600-25606400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr20:25605600-25606600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:25605600-25606600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr20:25605600-25606600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr20:25605600-25607400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr20:25605600-25608400	Weak transcription	Right Atrium	heart
11	chr20:25605600-25610000	Weak transcription	HSMMtube	muscle
12	chr20:25605600-25610200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr20:25605600-25610200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr20:25605600-25613000	Weak transcription	NHEK	skin
15	chr20:25605600-25615000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:25605600-25615000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr20:25605600-25615000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr20:25605600-25615200	Weak transcription	Adipose Nuclei	Adipose
19	chr20:25605600-25615200	Weak transcription	Brain Anterior Caudate	brain
20	chr20:25605600-25616000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:25605600-25616400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:25605600-25616400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr20:25605600-25616400	Weak transcription	Thymus	Thymus
24	chr20:25605600-25616600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:25605600-25616600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr20:25605600-25616800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr20:25605600-25616800	Weak transcription	Primary T cells from cord blood	blood
28	chr20:25605600-25616800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr20:25605600-25618000	Weak transcription	NH-A	brain
30	chr20:25605600-25619200	Weak transcription	Liver	Liver
31	chr20:25605600-25627000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr20:25605600-25628400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr20:25605600-25628600	Weak transcription	Colon Smooth Muscle	Colon
34	chr20:25605600-25630200	Weak transcription	Fetal Intestine Large	intestine
35	chr20:25605600-25635000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr20:25605600-25654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr20:25605800-25606400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:25605800-25606400	Flanking Active TSS	HepG2	liver
39	chr20:25605800-25616800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr20:25606000-25606600	Enhancers	Dnd41	blood
41	chr20:25606000-25606600	Flanking Active TSS	K562	blood
42	chr20:25606000-25607200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:25606000-25607600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr20:25606000-25612800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr20:25606000-25613200	Weak transcription	Hela-S3	cervix
46	chr20:25606200-25607400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr20:25606200-25616600	Weak transcription	Fetal Muscle Leg	muscle
48	chr20:25606200-25617600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr20:25606200-25626400	Weak transcription	A549	lung

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