Variant report

Variant	rs4241520
Chromosome Location	chr3:23997328-23997329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23957572..23960051-chr3:23995970..23999234,5	MCF-7	breast:
2	chr3:23956080..23959048-chr3:23995915..23997492,2	MCF-7	breast:
3	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11717862	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13091509	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13095392	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4131403	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4241514	0.83[EUR][1000 genomes]
rs4241515	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4241517	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4321479	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4589882	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4619734	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858094	0.81[EUR][1000 genomes]
rs4858095	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858098	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858551	0.81[EUR][1000 genomes]
rs4858553	0.81[EUR][1000 genomes]
rs4858565	0.87[EUR][1000 genomes]
rs4858567	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858569	0.91[ASN][1000 genomes]
rs62253379	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6419846	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6550814	0.93[ASN][1000 genomes]
rs6550815	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6550819	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6550823	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6550824	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6764154	0.81[EUR][1000 genomes]
rs6778783	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6779476	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6790557	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794922	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7371944	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7431301	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636810	0.91[ASN][1000 genomes]
rs9310725	0.82[EUR][1000 genomes]
rs9845287	0.81[EUR][1000 genomes]
rs9853532	0.90[ASN][1000 genomes]
rs9879378	0.81[EUR][1000 genomes]
rs9882735	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
2	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
5	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
9	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
10	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
15	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
16	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
18	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:23990400-23997600	Weak transcription	NH-A	brain
20	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:23991800-23999600	Weak transcription	HSMMtube	muscle
22	chr3:23992000-24000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:23992000-24001600	Weak transcription	Fetal Stomach	stomach
24	chr3:23992000-24007400	Weak transcription	Thymus	Thymus
25	chr3:23992200-23998400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:23992200-24000200	Weak transcription	HMEC	breast
27	chr3:23992200-24000400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:23992200-24001200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:23992200-24001400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:23992400-24002400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:23992400-24003400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:23992400-24003400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:23992400-24003400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:23992400-24017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:23993200-23999400	Weak transcription	Fetal Lung	lung
36	chr3:23993200-23999600	Weak transcription	A549	lung
37	chr3:23993400-23999400	Weak transcription	NHLF	lung
38	chr3:23993600-23999600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:23993600-24000200	Weak transcription	NHEK	skin
40	chr3:23993600-24000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:23993600-24009400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:23993600-24017800	Weak transcription	Brain Germinal Matrix	brain
43	chr3:23993800-23999600	Weak transcription	Gastric	stomach
44	chr3:23993800-23999600	Weak transcription	Pancreas	Pancrea
45	chr3:23993800-24001000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:23994000-24022800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:23994600-23998600	Enhancers	Stomach Mucosa	stomach
48	chr3:23995200-24003200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:23995200-24003200	Weak transcription	Dnd41	blood
50	chr3:23995200-24003400	Weak transcription	GM12878-XiMat	blood

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