Variant report

Variant	rs2424574
Chromosome Location	chr20:23608980-23608981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23608840..23610362-chr20:23612244..23613803,2	K562	blood:
2	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
3	chr20:23339592..23341756-chr20:23608896..23611631,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270001	Chromatin interaction
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2093145	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2104006	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2145233	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2145234	0.80[AFR][1000 genomes]
rs2180663	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2424566	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2424567	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2424576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424577	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]
rs2424581	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424588	0.83[AFR][1000 genomes]
rs2983603	0.81[EUR][1000 genomes]
rs2983605	0.83[AFR][1000 genomes]
rs2983636	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2983640	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2983644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3004144	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62208871	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs726217	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs911122	0.83[EUR][1000 genomes]
rs984503	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[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

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:23602000-23610000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:23602000-23610200	Weak transcription	Lung	lung
5	chr20:23602000-23612200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr20:23603800-23609200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr20:23603800-23609800	Weak transcription	Fetal Thymus	thymus
9	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:23604000-23609600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr20:23604000-23610200	Weak transcription	Ovary	ovary
12	chr20:23604000-23612200	Weak transcription	Liver	Liver
13	chr20:23604000-23612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:23604000-23613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr20:23604000-23613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr20:23604000-23613400	Weak transcription	Brain Hippocampus Middle	brain
17	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr20:23604200-23609200	Weak transcription	HUVEC	blood vessel
21	chr20:23604200-23609200	Weak transcription	Osteobl	bone
22	chr20:23604200-23609800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr20:23604200-23610000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr20:23604200-23615000	Weak transcription	Brain Anterior Caudate	brain
25	chr20:23604800-23609000	Weak transcription	Fetal Intestine Small	intestine
26	chr20:23604800-23612200	Weak transcription	Aorta	Aorta
27	chr20:23605000-23609200	Weak transcription	Adipose Nuclei	Adipose
28	chr20:23605000-23611800	Weak transcription	Fetal Muscle Leg	muscle
29	chr20:23605000-23612800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr20:23605200-23612200	Weak transcription	NHLF	lung
31	chr20:23605400-23609600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr20:23605400-23612200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr20:23606000-23609600	Weak transcription	NHDF-Ad	bronchial
34	chr20:23606600-23609400	Weak transcription	Psoas Muscle	Psoas
35	chr20:23606600-23609600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:23606600-23610400	Enhancers	HSMM	muscle
37	chr20:23606600-23615200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr20:23606800-23616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr20:23607000-23609200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr20:23607000-23609400	Weak transcription	Esophagus	oesophagus
42	chr20:23607000-23609800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:23607000-23612600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr20:23607000-23615000	Weak transcription	Colon Smooth Muscle	Colon
45	chr20:23607200-23609000	Weak transcription	GM12878-XiMat	blood
46	chr20:23607200-23609000	Weak transcription	HepG2	liver
47	chr20:23607200-23610800	Weak transcription	Right Atrium	heart
48	chr20:23607200-23612800	Weak transcription	Gastric	stomach
49	chr20:23607400-23609200	Weak transcription	Fetal Intestine Large	intestine
50	chr20:23607400-23609200	Weak transcription	Placenta	Placenta

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