Variant report

Variant	rs2339696
Chromosome Location	chr1:153480663-153480664
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:153478376..153480788-chr1:153481314..153483652,2	K562	blood:
2	chr1:153480033..153483904-chr1:153604458..153606849,3	K562	blood:
3	chr1:153479765..153482193-chr1:153627799..153629535,2	K562	blood:
4	chr1:153327311..153331799-chr1:153480650..153484791,7	MCF-7	breast:
5	chr1:153480481..153484963-chr1:153582556..153586017,6	MCF-7	breast:
6	chr1:153480132..153490926-chr1:153537975..153544732,26	MCF-7	breast:
7	chr1:153480135..153482234-chr1:153578835..153581505,2	MCF-7	breast:
8	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
9	chr1:153479337..153482179-chr1:153578655..153582224,3	MCF-7	breast:
10	chr1:153480409..153482467-chr1:153599959..153601900,2	MCF-7	breast:
11	chr1:153341060..153343420-chr1:153479644..153482399,2	MCF-7	breast:
12	chr1:153479500..153482310-chr1:153538620..153542576,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188643	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000160679	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs16835366	0.85[ASN][1000 genomes]
rs16835368	0.85[ASN][1000 genomes]
rs16835382	0.88[ASN][1000 genomes]
rs16835393	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17695220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887039	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964151	0.88[ASN][1000 genomes]
rs2094217	0.84[EUR][1000 genomes]
rs2094737	0.84[EUR][1000 genomes]
rs2094738	0.86[EUR][1000 genomes]
rs2248745	0.83[AMR][1000 genomes]
rs2262587	0.84[EUR][1000 genomes]
rs28410699	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464843	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483109	0.81[AMR][1000 genomes]
rs28632016	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28635377	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28676601	0.85[ASN][1000 genomes]
rs28707433	0.85[ASN][1000 genomes]
rs3762262	0.86[AMR][1000 genomes]
rs3915524	0.88[ASN][1000 genomes]
rs4017737	0.83[AMR][1000 genomes]
rs4272569	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4430277	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845351	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845352	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845548	0.85[ASN][1000 genomes]
rs4845549	0.88[ASN][1000 genomes]
rs4845550	0.88[ASN][1000 genomes]
rs4845551	0.88[ASN][1000 genomes]
rs4845552	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4845553	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4845554	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845555	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs532652	0.84[EUR][1000 genomes]
rs552446	0.86[AMR][1000 genomes]
rs585215	0.83[AMR][1000 genomes]
rs6587743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587745	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587746	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659403	0.86[AMR][1000 genomes]
rs6659755	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6660055	0.85[ASN][1000 genomes]
rs6679509	0.85[ASN][1000 genomes]
rs6684970	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690638	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6690712	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696893	0.89[ASN][1000 genomes]
rs7515940	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518306	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520093	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534343	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534347	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534830	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537898	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544359	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9426945	0.84[EUR][1000 genomes]
rs9427239	0.84[EUR][1000 genomes]
rs9427287	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9436094	0.85[ASN][1000 genomes]
rs9436095	0.82[AMR][1000 genomes];0.93[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 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	chr1:153477800-153480800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:153477800-153480800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:153477800-153481000	Enhancers	Fetal Muscle Leg	muscle
4	chr1:153477800-153481200	Enhancers	Ovary	ovary
5	chr1:153478000-153481000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:153478000-153481000	Enhancers	Colon Smooth Muscle	Colon
7	chr1:153478000-153481000	Enhancers	HSMM	muscle
8	chr1:153478000-153481200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:153478000-153481200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:153478000-153482200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:153478000-153482600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:153478400-153481000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:153478400-153481000	Enhancers	NHLF	lung
14	chr1:153478800-153480800	Enhancers	Fetal Intestine Large	intestine
15	chr1:153478800-153480800	Enhancers	Fetal Stomach	stomach
16	chr1:153478800-153481000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:153478800-153481000	Enhancers	Fetal Intestine Small	intestine
18	chr1:153478800-153481000	Enhancers	NH-A	brain
19	chr1:153478800-153481200	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:153478800-153482200	Enhancers	NHEK	skin
21	chr1:153478800-153482400	Enhancers	HMEC	breast
22	chr1:153479000-153480800	Enhancers	Colonic Mucosa	Colon
23	chr1:153479000-153481000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:153479200-153482000	Weak transcription	Spleen	Spleen
25	chr1:153479200-153485200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:153479200-153487600	Weak transcription	Small Intestine	intestine
27	chr1:153479600-153483400	Weak transcription	K562	blood
28	chr1:153479800-153482200	Weak transcription	Pancreas	Pancrea
29	chr1:153479800-153483200	Weak transcription	Placenta	Placenta
30	chr1:153479800-153483200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:153479800-153483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:153479800-153488000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:153480000-153480800	Enhancers	NHDF-Ad	bronchial
34	chr1:153480000-153481200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:153480000-153481200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:153480000-153481200	Enhancers	Osteobl	bone
37	chr1:153480000-153481400	Enhancers	A549	lung
38	chr1:153480000-153482800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:153480200-153480800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:153480200-153480800	Enhancers	HepG2	liver
41	chr1:153480200-153482400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:153480200-153483200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:153480200-153483400	Weak transcription	Hela-S3	cervix
44	chr1:153480200-153483600	Weak transcription	Stomach Mucosa	stomach
45	chr1:153480200-153488000	Weak transcription	Left Ventricle	heart
46	chr1:153480400-153483200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:153480400-153483400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:153480400-153483600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:153480600-153482000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:153480600-153483400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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