Variant report

Variant	rs4666359
Chromosome Location	chr2:20335614-20335615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20335576..20338444-chr2:20340414..20343314,2	MCF-7	breast:
2	chr2:20331753..20338544-chr2:20423396..20426851,7	MCF-7	breast:
3	chr2:20333229..20337003-chr2:20421997..20425401,4	MCF-7	breast:
4	chr2:20155364..20156194-chr2:20335109..20335818,2	MCF-7	breast:
5	chr2:20335273..20335962-chr2:20425157..20425727,2	MCF-7	breast:
6	chr2:20335122..20335719-chr2:20442089..20442630,2	K562	blood:
7	chr2:20322072..20326084-chr2:20334448..20336577,3	MCF-7	breast:
8	chr2:20334225..20337843-chr2:20372187..20375546,3	MCF-7	breast:
9	chr2:20335050..20336054-chr2:20390851..20391800,4	MCF-7	breast:
10	chr2:20306514..20307389-chr2:20335072..20336127,3	MCF-7	breast:
11	chr2:20335194..20335984-chr2:20390827..20391610,3	MCF-7	breast:
12	chr2:20329969..20331497-chr2:20335447..20338002,2	MCF-7	breast:
13	chr2:20329242..20332304-chr2:20334345..20337488,3	MCF-7	breast:
14	chr2:20335603..20338539-chr2:20339889..20342133,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234378	Chromatin interaction
ENSG00000266059	Chromatin interaction
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10196396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4666358	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4666360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666361	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20326400-20336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:20331200-20335800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20331600-20337000	Weak transcription	Colonic Mucosa	Colon
4	chr2:20331800-20338600	Weak transcription	Small Intestine	intestine
5	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:20334200-20346600	Enhancers	Placenta	Placenta
7	chr2:20334800-20336200	Enhancers	Esophagus	oesophagus
8	chr2:20335000-20336000	Enhancers	Liver	Liver
9	chr2:20335000-20336800	Bivalent Enhancer	HepG2	liver
10	chr2:20335000-20337200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:20335200-20335800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:20335200-20336000	Enhancers	Fetal Muscle Trunk	muscle
13	chr2:20335200-20336200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:20335200-20336200	Enhancers	GM12878-XiMat	blood
15	chr2:20335400-20335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:20335400-20336000	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:20335400-20336200	Enhancers	Stomach Mucosa	stomach
18	chr2:20335400-20336400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:20335400-20339800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:20335600-20335800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr2:20335600-20335800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:20335600-20335800	Enhancers	Fetal Kidney	kidney
23	chr2:20335600-20336000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:20335600-20336000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:20335600-20336000	Enhancers	Fetal Intestine Small	intestine
26	chr2:20335600-20336000	Enhancers	Fetal Lung	lung
27	chr2:20335600-20336000	Enhancers	A549	lung
28	chr2:20335600-20336200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:20335600-20336400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr2:20335600-20336400	Enhancers	HMEC	breast
31	chr2:20335600-20337000	Enhancers	NHEK	skin
32	chr2:20335600-20337600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:20335600-20337800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:20335600-20339200	Enhancers	K562	blood

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