Variant report

Variant	rs2424577
Chromosome Location	chr20:23613750-23613751
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	POLR2A	chr20:23611823-23615036	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
3	HEY1	chr20:23612370-23614357	HepG2	liver:	n/a	chr20:23612700-23612715
4	MAFK	chr20:23613449-23613772	HepG2	liver:	n/a	chr20:23613494-23613505 chr20:23613494-23613505 chr20:23613495-23613506 chr20:23613493-23613507 chr20:23613494-23613510
5	POLR2A	chr20:23613572-23614260	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr20:23611815-23614265	HepG2	liver:	n/a	n/a
7	HEY1	chr20:23613414-23613928	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	NFIC	chr20:23613243-23613947	HepG2	liver:	n/a	n/a
12	POLR2A	chr20:23612536-23614248	HepG2	liver:	n/a	n/a
13	POLR2A	chr20:23609430-23615030	HepG2	liver:	n/a	n/a

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

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

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2093145	0.88[EUR][1000 genomes]
rs2104006	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2145233	0.83[EUR][1000 genomes]
rs2145234	0.80[EUR][1000 genomes]
rs2180663	0.81[EUR][1000 genomes]
rs2424566	0.90[EUR][1000 genomes]
rs2424567	0.90[EUR][1000 genomes]
rs2424574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424581	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2424588	0.80[EUR][1000 genomes]
rs2983603	0.82[EUR][1000 genomes]
rs2983605	0.80[EUR][1000 genomes]
rs2983636	0.88[EUR][1000 genomes]
rs2983640	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2983644	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs3004144	0.87[EUR][1000 genomes]
rs62208871	0.82[EUR][1000 genomes]
rs726217	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs911122	0.84[EUR][1000 genomes]
rs984503	0.88[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2424577	CST3	cis	cerebellum	SCAN
rs2424577	CST3	cis	parietal	SCAN

Chromatin state (count:101 , 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	chr20:23610000-23613800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr20:23610200-23617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:23610200-23617000	Weak transcription	K562	blood
20	chr20:23610400-23613800	Weak transcription	Psoas Muscle	Psoas
21	chr20:23610400-23615400	Weak transcription	NHDF-Ad	bronchial
22	chr20:23610400-23616000	Weak transcription	Fetal Thymus	thymus
23	chr20:23610400-23616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr20:23610400-23616800	Weak transcription	NH-A	brain
25	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr20:23610600-23614400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:23610600-23616800	Weak transcription	Hela-S3	cervix
28	chr20:23610800-23615200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:23610800-23616800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:23610800-23617400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr20:23611000-23615600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr20:23611000-23616000	Strong transcription	Fetal Intestine Small	intestine
33	chr20:23611200-23614000	Weak transcription	Stomach Mucosa	stomach
34	chr20:23611200-23615000	Weak transcription	Right Atrium	heart
35	chr20:23611200-23615800	Weak transcription	GM12878-XiMat	blood
36	chr20:23611400-23615600	Weak transcription	HUVEC	blood vessel
37	chr20:23611800-23613800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr20:23612000-23615000	Strong transcription	Brain Germinal Matrix	brain
39	chr20:23612000-23615000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr20:23612000-23615400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr20:23612000-23615600	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr20:23612000-23615600	Strong transcription	Fetal Intestine Large	intestine
43	chr20:23612000-23617000	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr20:23612200-23614000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr20:23612200-23614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr20:23612200-23614800	Strong transcription	Right Ventricle	heart
47	chr20:23612200-23614800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr20:23612200-23614800	Strong transcription	Spleen	Spleen
49	chr20:23612200-23615000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr20:23612200-23615000	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links