Variant report

Variant	rs1001215
Chromosome Location	chr2:10124280-10124281
allele	G/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	chr2:10091162..10093272-chr2:10122977..10125313,2	MCF-7	breast:
2	chr2:10124031..10125985-chr2:10182385..10183963,2	MCF-7	breast:
3	chr2:10118579..10121922-chr2:10122054..10125273,3	K562	blood:
4	chr2:10123969..10126357-chr2:10126821..10128999,2	MCF-7	breast:
5	chr2:10124029..10125034-chr2:10188472..10189404,3	MCF-7	breast:
6	chr2:10124090..10124739-chr2:10237291..10238060,2	MCF-7	breast:
7	chr2:10111585..10113356-chr2:10123202..10126710,3	K562	blood:
8	chr2:10122873..10124837-chr2:10586757..10588476,2	K562	blood:
9	chr2:10119057..10121922-chr2:10123491..10126489,3	K562	blood:
10	chr2:9939472..9940257-chr2:10124055..10124606,2	MCF-7	breast:
11	chr2:10121725..10124609-chr2:10134355..10135987,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115758	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000134317	Chromatin interaction
ENSG00000206633	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11893362	0.94[ASN][1000 genomes]
rs12472800	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12475243	0.93[ASN][1000 genomes]
rs12614084	0.91[ASN][1000 genomes]
rs12616347	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618788	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12623004	0.94[ASN][1000 genomes]
rs1367383	0.94[ASN][1000 genomes]
rs1367384	0.94[ASN][1000 genomes]
rs1367388	0.93[ASN][1000 genomes]
rs1367389	0.93[ASN][1000 genomes]
rs1430621	0.93[ASN][1000 genomes]
rs1549752	0.94[ASN][1000 genomes]
rs1549753	0.93[ASN][1000 genomes]
rs1549754	0.93[ASN][1000 genomes]
rs1820964	0.94[ASN][1000 genomes]
rs1835424	0.92[ASN][1000 genomes]
rs1897165	0.94[ASN][1000 genomes]
rs2011516	0.94[ASN][1000 genomes]
rs2011523	0.94[ASN][1000 genomes]
rs2033324	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2033325	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2033326	0.94[ASN][1000 genomes]
rs2303920	0.94[ASN][1000 genomes]
rs28444564	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34629102	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34950562	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35321554	0.88[EUR][1000 genomes]
rs35341467	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35646916	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35816086	0.85[EUR][1000 genomes]
rs36033432	0.94[ASN][1000 genomes]
rs3762536	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3762537	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3762538	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3791753	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3791758	0.94[ASN][1000 genomes]
rs3791760	0.91[ASN][1000 genomes]
rs3828260	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4610026	0.92[ASN][1000 genomes]
rs4669508	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4669511	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6432047	0.94[ASN][1000 genomes]
rs6432048	0.94[ASN][1000 genomes]
rs6714600	0.94[ASN][1000 genomes]
rs6743918	0.94[ASN][1000 genomes]
rs72784422	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72784424	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72784425	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs731453	0.95[ASN][1000 genomes]
rs7596288	0.89[ASN][1000 genomes]
rs891500	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10094800-10124400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
3	chr2:10101600-10136400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:10102200-10136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:10104600-10130200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:10113400-10130800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:10113400-10136800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:10113400-10141200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:10113800-10124600	Weak transcription	Fetal Kidney	kidney
10	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:10116800-10124400	Weak transcription	Right Ventricle	heart
12	chr2:10116800-10125000	Weak transcription	Right Atrium	heart
13	chr2:10116800-10126200	Weak transcription	Esophagus	oesophagus
14	chr2:10118800-10124400	Weak transcription	Liver	Liver
15	chr2:10119400-10126000	Enhancers	Osteobl	bone
16	chr2:10119600-10125800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:10119600-10126400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:10120400-10131800	Weak transcription	Dnd41	blood
19	chr2:10120600-10124400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:10120600-10125800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:10121000-10124400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:10121200-10128000	Weak transcription	Fetal Brain Male	brain
23	chr2:10121600-10127000	Weak transcription	HepG2	liver
24	chr2:10122200-10126000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:10122600-10125000	Enhancers	Fetal Muscle Leg	muscle
26	chr2:10122600-10125200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:10122600-10126200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:10122600-10126400	Enhancers	Adipose Nuclei	Adipose
29	chr2:10122800-10126000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:10123000-10124400	Weak transcription	HSMMtube	muscle
31	chr2:10123000-10126400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:10123200-10124600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:10123200-10125200	Enhancers	Fetal Muscle Trunk	muscle
34	chr2:10123400-10124400	Weak transcription	NHLF	lung
35	chr2:10123400-10124600	Weak transcription	HSMM	muscle
36	chr2:10123400-10126200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:10123400-10126200	Enhancers	NHDF-Ad	bronchial
38	chr2:10123400-10126400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:10123800-10125000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:10124000-10124400	Weak transcription	NH-A	brain
41	chr2:10124000-10125400	Enhancers	Placenta	Placenta
42	chr2:10124000-10136400	Weak transcription	Hela-S3	cervix
43	chr2:10124200-10124400	Enhancers	Gastric	stomach
44	chr2:10124200-10124400	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr2:10124200-10124400	Enhancers	K562	blood
46	chr2:10124200-10124600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:10124200-10124600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:10124200-10124600	Enhancers	Brain Substantia Nigra	brain
49	chr2:10124200-10124600	Enhancers	Fetal Intestine Small	intestine
50	chr2:10124200-10124800	Enhancers	Primary B cells from peripheral blood	blood

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