Variant report

Variant	rs4942798
Chromosome Location	chr13:49598189-49598190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49548397..49551326-chr13:49595569..49598537,2	MCF-7	breast:
2	chr13:49597126..49599869-chr13:49609048..49611243,2	MCF-7	breast:
3	chr13:49596195..49598292-chr13:49601731..49604447,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102531	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs12872974	0.86[EUR][1000 genomes]
rs1359066	0.86[EUR][1000 genomes]
rs1407829	0.83[EUR][1000 genomes]
rs1928109	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1928110	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1937180	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2021622	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2026029	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2146748	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2149498	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181537	0.85[EUR][1000 genomes]
rs2181538	0.85[EUR][1000 genomes]
rs2181539	0.85[EUR][1000 genomes]
rs2183095	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2407265	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2407266	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2897633	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2987528	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987532	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2987535	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2994377	0.84[EUR][1000 genomes]
rs2994378	0.84[EUR][1000 genomes]
rs2994379	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2994380	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2994381	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3012116	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012117	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3012118	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012121	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3012127	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3012133	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3012135	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3012136	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4142065	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4258502	0.83[ASN][1000 genomes]
rs4530025	0.84[EUR][1000 genomes]
rs4942795	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942796	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942799	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4942800	0.87[EUR][1000 genomes]
rs6561491	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561493	0.87[EUR][1000 genomes]
rs6561496	0.85[EUR][1000 genomes]
rs7139854	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs720627	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs728075	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7318871	0.86[EUR][1000 genomes]
rs7325026	0.84[EUR][1000 genomes]
rs7328000	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7329291	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7331917	0.83[EUR][1000 genomes]
rs7983885	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7986624	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7987258	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7988168	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7994910	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7995616	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997118	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7998359	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7999513	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316426	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316427	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9316428	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316429	0.86[ASN][1000 genomes]
rs9526517	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526518	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526520	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526521	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535126	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9535133	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535136	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535140	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9535141	0.87[EUR][1000 genomes]
rs9535145	0.83[EUR][1000 genomes]
rs9535146	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535147	0.86[EUR][1000 genomes]
rs9535149	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9562866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568143	0.82[ASN][1000 genomes]
rs9568150	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9568151	0.85[EUR][1000 genomes]
rs9591235	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv900068	chr13:49559790-49605774	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1803100	chr13:49576474-49655941	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49557000-49626800	Weak transcription	Right Ventricle	heart
3	chr13:49568000-49598200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr13:49568800-49626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:49568800-49627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:49572000-49604800	Weak transcription	Aorta	Aorta
7	chr13:49573400-49634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr13:49581800-49606000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr13:49582000-49601200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:49582200-49659000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr13:49582800-49617600	Weak transcription	Liver	Liver
12	chr13:49584000-49616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:49584200-49649200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr13:49584600-49599400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr13:49584600-49602600	Weak transcription	Thymus	Thymus
16	chr13:49584600-49613800	Weak transcription	Left Ventricle	heart
17	chr13:49584800-49612400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:49587400-49602400	Weak transcription	Fetal Intestine Small	intestine
19	chr13:49587800-49605200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr13:49587800-49611400	Weak transcription	Fetal Kidney	kidney
21	chr13:49587800-49626600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr13:49592800-49649600	Weak transcription	Fetal Intestine Large	intestine
23	chr13:49593000-49604800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:49593400-49611800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr13:49593800-49603000	Weak transcription	Placenta	Placenta
26	chr13:49594600-49599000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr13:49594800-49598200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:49594800-49636000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr13:49595000-49603800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr13:49595200-49600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:49595400-49598600	Enhancers	Osteobl	bone
32	chr13:49595400-49599000	Enhancers	HMEC	breast
33	chr13:49595800-49599800	Enhancers	NHEK	skin
34	chr13:49596400-49598800	ZNF genes & repeats	Dnd41	blood
35	chr13:49596400-49599600	Weak transcription	NHLF	lung
36	chr13:49596400-49611600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:49596400-49626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:49596600-49598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:49596800-49599000	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr13:49596800-49600200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:49596800-49606600	Weak transcription	HepG2	liver
42	chr13:49596800-49609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr13:49597000-49598400	Weak transcription	Hela-S3	cervix
44	chr13:49597000-49598400	Weak transcription	HSMM	muscle
45	chr13:49597000-49606000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr13:49597200-49598600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:49597200-49598800	Enhancers	A549	lung
48	chr13:49597200-49619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr13:49597200-49626600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr13:49597400-49598200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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