Variant report

Variant	rs10440023
Chromosome Location	chr3:159504674-159504675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:159480418..159485166-chr3:159503972..159508876,8	MCF-7	breast:
2	chr3:159504199..159507462-chr3:159515627..159518397,3	MCF-7	breast:
3	chr3:159504230..159507022-chr3:159529536..159532354,2	MCF-7	breast:
4	chr3:159504063..159506884-chr3:159510912..159512830,2	K562	blood:
5	chr3:159487312..159489793-chr3:159503414..159505696,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10470474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470475	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13314923	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28695486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4621369	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56786891	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015941	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015943	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73015967	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017937	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73017960	1.00[EUR][1000 genomes]
rs7612849	1.00[EUR][1000 genomes]
rs7615917	0.83[AMR][1000 genomes]
rs7651449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9811600	0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814058	1.00[EUR][1000 genomes]
rs9816506	0.83[AMR][1000 genomes]
rs9830331	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832139	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9845205	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845849	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846819	1.00[EUR][1000 genomes]
rs9850723	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853947	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855171	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872127	0.83[AMR][1000 genomes]
rs9877761	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878860	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9880866	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159484400-159505400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:159493600-159505200	Weak transcription	Lung	lung
3	chr3:159493600-159505400	Weak transcription	Fetal Stomach	stomach
4	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:159499800-159506400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:159500400-159509200	Enhancers	HepG2	liver
8	chr3:159501000-159508000	Enhancers	Colon Smooth Muscle	Colon
9	chr3:159501200-159506200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:159501800-159507600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:159501800-159510200	Enhancers	Fetal Intestine Large	intestine
12	chr3:159502000-159504800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:159502000-159505000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:159502000-159505200	Enhancers	Hela-S3	cervix
15	chr3:159502000-159522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:159502200-159509000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:159502400-159505000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:159502400-159506800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:159502400-159508000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:159502400-159508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:159502600-159504800	Enhancers	HUVEC	blood vessel
22	chr3:159502600-159506400	Enhancers	Osteobl	bone
23	chr3:159502800-159505600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr3:159502800-159506000	Enhancers	HMEC	breast
25	chr3:159502800-159506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:159502800-159508000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:159503000-159505000	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:159503000-159505000	Enhancers	NH-A	brain
29	chr3:159503000-159506200	Enhancers	NHDF-Ad	bronchial
30	chr3:159503000-159506400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:159503000-159506400	Enhancers	NHLF	lung
32	chr3:159503000-159510200	Enhancers	Fetal Intestine Small	intestine
33	chr3:159503200-159505400	Enhancers	HSMM	muscle
34	chr3:159503200-159506200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:159503400-159504800	Weak transcription	Fetal Lung	lung
36	chr3:159503400-159505200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:159503400-159505800	Weak transcription	Fetal Kidney	kidney
38	chr3:159503400-159508000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:159503600-159506400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:159503600-159508000	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:159503800-159509600	Enhancers	Adipose Nuclei	Adipose
42	chr3:159504000-159518600	Enhancers	Brain Hippocampus Middle	brain
43	chr3:159504200-159518400	Enhancers	Brain Substantia Nigra	brain
44	chr3:159504400-159504800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:159504400-159504800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:159504400-159504800	Enhancers	GM12878-XiMat	blood
47	chr3:159504400-159505000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:159504400-159505000	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:159504400-159505000	Flanking Active TSS	A549	lung
50	chr3:159504400-159505200	Enhancers	H9 Cell Line	embryonic stem cell

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