Variant report

Variant	rs2424578
Chromosome Location	chr20:23614087-23614088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23613786-23614099	K562	blood:	n/a	n/a
2	POLR2A	chr20:23611823-23615036	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
4	HEY1	chr20:23612370-23614357	HepG2	liver:	n/a	chr20:23612700-23612715
5	POLR2A	chr20:23613872-23614267	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:23613572-23614260	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr20:23611815-23614265	HepG2	liver:	n/a	n/a
8	POLR2A	chr20:23611753-23618814	HepG2	liver:	n/a	n/a
9	POLR2A	chr20:23610050-23614159	K562	blood:	n/a	n/a
10	POLR2A	chr20:23611797-23614289	HepG2	liver:	n/a	n/a
11	POLR2A	chr20:23612536-23614248	HepG2	liver:	n/a	n/a
12	POLR2A	chr20:23609430-23615030	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23610507..23612555-chr20:23613561..23616038,2	MCF-7	breast:
2	chr20:23604645..23607070-chr20:23613987..23616956,2	K562	blood:
3	chr20:23332367..23335198-chr20:23611839..23614673,2	MCF-7	breast:
4	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270001	TF binding region
ENSG00000269407	Chromatin interaction
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1158166	0.81[YRI][hapmap]
rs2424579	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2983637	0.89[AFR][1000 genomes]
rs3004146	0.86[YRI][hapmap];0.89[AFR][1000 genomes]
rs3004147	0.81[YRI][hapmap]
rs911127	0.89[AFR][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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:23604200-23615000	Weak transcription	Brain Anterior Caudate	brain
8	chr20:23606600-23615200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:23606800-23616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:23607000-23615000	Weak transcription	Colon Smooth Muscle	Colon
12	chr20:23607600-23615400	Weak transcription	Fetal Kidney	kidney
13	chr20:23608200-23614400	Weak transcription	Thymus	Thymus
14	chr20:23609600-23615000	Weak transcription	HSMMtube	muscle
15	chr20:23609800-23616800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr20:23610200-23617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr20:23610200-23617000	Weak transcription	K562	blood
19	chr20:23610400-23615400	Weak transcription	NHDF-Ad	bronchial
20	chr20:23610400-23616000	Weak transcription	Fetal Thymus	thymus
21	chr20:23610400-23616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr20:23610400-23616800	Weak transcription	NH-A	brain
23	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr20:23610600-23614400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr20:23610600-23616800	Weak transcription	Hela-S3	cervix
26	chr20:23610800-23615200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:23610800-23616800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr20:23610800-23617400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr20:23611000-23615600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr20:23611000-23616000	Strong transcription	Fetal Intestine Small	intestine
31	chr20:23611200-23615000	Weak transcription	Right Atrium	heart
32	chr20:23611200-23615800	Weak transcription	GM12878-XiMat	blood
33	chr20:23611400-23615600	Weak transcription	HUVEC	blood vessel
34	chr20:23612000-23615000	Strong transcription	Brain Germinal Matrix	brain
35	chr20:23612000-23615000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
36	chr20:23612000-23615400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr20:23612000-23615600	Genic enhancers	Primary monocytes fromperipheralblood	blood
38	chr20:23612000-23615600	Strong transcription	Fetal Intestine Large	intestine
39	chr20:23612000-23617000	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr20:23612200-23614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr20:23612200-23614800	Strong transcription	Right Ventricle	heart
42	chr20:23612200-23614800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr20:23612200-23614800	Strong transcription	Spleen	Spleen
44	chr20:23612200-23615000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr20:23612200-23615000	Strong transcription	Liver	Liver
46	chr20:23612200-23615000	Strong transcription	Left Ventricle	heart
47	chr20:23612200-23615200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:23612200-23615200	Strong transcription	Esophagus	oesophagus
49	chr20:23612200-23615400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr20:23612200-23615400	Strong transcription	NHLF	lung

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