Variant report

Variant	rs12652168
Chromosome Location	chr5:52335494-52335495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52285122..52287993-chr5:52333837..52337640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1062535	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10940290	0.81[EUR][1000 genomes]
rs1126643	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11959632	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12515364	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12517446	0.84[ASN][1000 genomes]
rs12518279	0.89[ASN][1000 genomes]
rs12521915	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12657429	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12657501	0.83[AFR][1000 genomes]
rs12657972	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1316250	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1363192	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1421929	0.90[ASN][1000 genomes]
rs1421930	0.90[ASN][1000 genomes]
rs1421931	0.90[ASN][1000 genomes]
rs1421932	0.90[ASN][1000 genomes]
rs1421937	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1445943	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16880669	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1833558	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1862191	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991013	0.87[ASN][1000 genomes]
rs2075615	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2075616	0.88[ASN][1000 genomes]
rs2075617	0.87[ASN][1000 genomes]
rs2287871	0.88[ASN][1000 genomes]
rs2303122	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2303123	0.80[ASN][1000 genomes]
rs2303127	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2897458	0.90[ASN][1000 genomes]
rs2910964	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2910965	0.90[ASN][1000 genomes]
rs2910971	0.90[ASN][1000 genomes]
rs2974976	0.90[ASN][1000 genomes]
rs2974978	0.90[ASN][1000 genomes]
rs2974987	0.90[ASN][1000 genomes]
rs3212424	0.81[EUR][1000 genomes]
rs3212438	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212439	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212441	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212450	0.82[EUR][1000 genomes]
rs3212453	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212455	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212457	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212458	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212461	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212464	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212467	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3212472	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212478	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212480	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212481	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212486	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3212508	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3212509	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3212522	0.90[ASN][1000 genomes]
rs3212527	0.90[ASN][1000 genomes]
rs3212533	0.90[ASN][1000 genomes]
rs3212591	0.89[ASN][1000 genomes]
rs3212600	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3212601	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3212619	0.86[ASN][1000 genomes]
rs3212640	0.84[ASN][1000 genomes]
rs3756537	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3776787	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3797495	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3797496	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3797498	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3822558	0.82[EUR][1000 genomes]
rs3926397	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62357232	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62357233	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67719154	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6898333	0.83[ASN][1000 genomes]
rs7725246	0.83[ASN][1000 genomes]
rs984966	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs989073	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs990602	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv881217	chr5:52334774-52341512	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:52328800-52335800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
7	chr5:52329400-52335600	Weak transcription	Dnd41	blood
8	chr5:52331000-52336200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:52331000-52337000	Weak transcription	Fetal Kidney	kidney
10	chr5:52331800-52337200	Enhancers	HUVEC	blood vessel
11	chr5:52333400-52337000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:52333400-52341400	Strong transcription	HepG2	liver
13	chr5:52333600-52336800	Weak transcription	Fetal Lung	lung
14	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
16	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
18	chr5:52334200-52337000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:52334400-52335600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:52334400-52336200	Enhancers	HMEC	breast
21	chr5:52334400-52337000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:52334400-52338000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:52334600-52336000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:52334600-52336400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:52334600-52336400	Enhancers	Hela-S3	cervix
27	chr5:52334600-52337000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:52334600-52337000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:52334600-52337000	Weak transcription	A549	lung
30	chr5:52334600-52337000	Weak transcription	NH-A	brain
31	chr5:52334600-52337000	Weak transcription	NHDF-Ad	bronchial
32	chr5:52334600-52337000	Weak transcription	NHLF	lung
33	chr5:52334600-52337000	Weak transcription	Osteobl	bone
34	chr5:52334600-52337400	Weak transcription	Adipose Nuclei	Adipose
35	chr5:52334600-52343400	Weak transcription	Gastric	stomach
36	chr5:52334600-52348400	Weak transcription	Lung	lung
37	chr5:52334800-52337000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:52334800-52337000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:52334800-52337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:52334800-52343400	Weak transcription	Esophagus	oesophagus
41	chr5:52334800-52343800	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:52334800-52343800	Weak transcription	Pancreas	Pancrea
43	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
44	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
45	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:52335000-52336600	Enhancers	NHEK	skin
47	chr5:52335200-52337000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:52335200-52337800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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