Variant report

Variant	rs4666366
Chromosome Location	chr2:20340155-20340156
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:20339624..20342165-chr2:20377427..20379627,2	MCF-7	breast:
2	chr2:20339085..20342472-chr2:20423040..20426364,5	MCF-7	breast:
3	chr2:20337846..20345492-chr2:20421951..20427912,20	MCF-7	breast:
4	chr2:20335603..20338539-chr2:20339889..20342133,4	K562	blood:
5	chr2:20337265..20341089-chr2:20350774..20352905,3	MCF-7	breast:
6	chr2:20332851..20335555-chr2:20339124..20341592,3	K562	blood:
7	chr2:20337465..20342202-chr2:20382545..20388364,6	MCF-7	breast:
8	chr2:20302794..20305910-chr2:20337863..20340597,3	MCF-7	breast:
9	chr2:20338207..20341164-chr2:20430015..20431577,2	MCF-7	breast:
10	chr2:20338664..20345614-chr2:20377409..20381353,9	MCF-7	breast:
11	chr2:20339841..20342282-chr2:20379713..20382419,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11678155	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090033	1.00[CHB][hapmap]
rs2348314	0.80[GIH][hapmap]
rs4666368	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6531209	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6531212	0.80[GIH][hapmap]
rs7563386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973129	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975950	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20334200-20346600	Enhancers	Placenta	Placenta
3	chr2:20335800-20343400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:20336000-20340600	Weak transcription	Liver	Liver
5	chr2:20336400-20346200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:20336800-20340200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:20336800-20341800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:20337200-20340600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:20337400-20343400	Enhancers	NHEK	skin
10	chr2:20337800-20340200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:20337800-20341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:20338000-20340800	Enhancers	Hela-S3	cervix
13	chr2:20338000-20345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:20338000-20346800	Enhancers	HMEC	breast
15	chr2:20338200-20342200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:20338400-20342000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:20338600-20340400	Enhancers	Fetal Intestine Large	intestine
18	chr2:20338600-20340800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:20338600-20341000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:20338600-20341200	Enhancers	A549	lung
21	chr2:20338800-20340200	Enhancers	Fetal Intestine Small	intestine
22	chr2:20338800-20340800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:20339000-20340600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:20339000-20340600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:20339000-20340600	Weak transcription	NH-A	brain
26	chr2:20339000-20340600	Weak transcription	NHLF	lung
27	chr2:20339200-20340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:20339200-20340800	Weak transcription	Osteobl	bone
29	chr2:20339200-20341200	Weak transcription	K562	blood
30	chr2:20339400-20340200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:20339400-20340200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:20339400-20340600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:20339400-20341000	Weak transcription	Spleen	Spleen
34	chr2:20339400-20341600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:20339600-20340400	Enhancers	Fetal Muscle Trunk	muscle
36	chr2:20339600-20340600	Weak transcription	Esophagus	oesophagus
37	chr2:20339600-20340800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:20339600-20341000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:20339600-20341800	Bivalent Enhancer	HepG2	liver
40	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
41	chr2:20339800-20340800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:20339800-20340800	Weak transcription	Stomach Mucosa	stomach
43	chr2:20339800-20340800	Weak transcription	HSMM	muscle
44	chr2:20339800-20341000	Weak transcription	Colonic Mucosa	Colon
45	chr2:20339800-20341000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:20339800-20341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:20340000-20340400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:20340000-20340400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:20340000-20341200	Weak transcription	HSMMtube	muscle

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