Variant report

Variant	rs6852148
Chromosome Location	chr4:53750002-53750003
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	chr4:53578381..53580199-chr4:53748733..53750855,2	MCF-7	breast:
2	chr4:53715465..53717915-chr4:53748773..53751088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226950	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10001855	0.94[ASN][1000 genomes]
rs10008073	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs10014464	0.85[ASN][1000 genomes]
rs10032190	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1043975	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1047959	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs10866413	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs11930907	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11934293	0.85[ASN][1000 genomes]
rs11940297	0.88[ASN][1000 genomes]
rs11941562	0.87[ASN][1000 genomes]
rs1483685	0.85[ASN][1000 genomes]
rs1483686	0.81[JPT][hapmap]
rs17082081	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs17082143	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17082147	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1963003	0.85[ASN][1000 genomes]
rs2003198	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2017237	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046364	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062253	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2200226	0.90[ASN][1000 genomes]
rs2279334	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2306601	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2411281	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28419463	0.84[ASN][1000 genomes]
rs28704139	0.85[ASN][1000 genomes]
rs2898681	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs301090	0.80[ASN][1000 genomes]
rs301119	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs301123	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs301135	0.85[JPT][hapmap]
rs4864679	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4864681	0.87[ASN][1000 genomes]
rs4864682	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4864683	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4864688	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864691	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59649036	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61268502	0.89[ASN][1000 genomes]
rs62336785	0.85[ASN][1000 genomes]
rs62336790	0.80[EUR][1000 genomes]
rs62336791	0.89[ASN][1000 genomes]
rs62336792	0.88[ASN][1000 genomes]
rs62336794	0.93[ASN][1000 genomes]
rs62336795	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62336823	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6833096	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839084	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73143042	0.85[ASN][1000 genomes]
rs8287	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs900607	0.93[ASN][1000 genomes]
rs922932	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs922933	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9646	0.91[ASN][1000 genomes]
rs9993034	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
2	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
3	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
4	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:53731400-53751000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:53732400-53750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:53732400-53755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:53733000-53767800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr4:53733200-53759000	Weak transcription	Osteobl	bone
10	chr4:53733600-53750200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:53734200-53760800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:53735000-53770200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:53735200-53755200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:53735200-53778000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:53735600-53751600	Weak transcription	Spleen	Spleen
17	chr4:53735800-53772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:53736000-53750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:53736000-53752600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:53736200-53758800	Weak transcription	NHLF	lung
21	chr4:53736400-53752200	Weak transcription	Adipose Nuclei	Adipose
22	chr4:53736600-53759600	Weak transcription	Ovary	ovary
23	chr4:53736600-53785600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:53736800-53750800	Weak transcription	Brain Angular Gyrus	brain
25	chr4:53737200-53750600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:53737200-53751200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:53737200-53779200	Weak transcription	Gastric	stomach
28	chr4:53737600-53756000	Weak transcription	NHDF-Ad	bronchial
29	chr4:53738800-53753400	Weak transcription	Liver	Liver
30	chr4:53740000-53750800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:53740200-53750200	Weak transcription	Stomach Mucosa	stomach
32	chr4:53740600-53751800	Weak transcription	Brain Substantia Nigra	brain
33	chr4:53740600-53752200	Weak transcription	Fetal Intestine Large	intestine
34	chr4:53740800-53752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:53740800-53753200	Weak transcription	Brain Anterior Caudate	brain
36	chr4:53741000-53757400	Weak transcription	Pancreas	Pancrea
37	chr4:53741000-53757800	Weak transcription	Fetal Lung	lung
38	chr4:53741800-53757800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:53742400-53754800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:53742600-53752400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:53743400-53771000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr4:53743600-53752200	Weak transcription	Left Ventricle	heart
43	chr4:53743600-53758200	Weak transcription	Psoas Muscle	Psoas
44	chr4:53743600-53770200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:53744000-53758000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:53744200-53750400	Weak transcription	Fetal Stomach	stomach
47	chr4:53744200-53752000	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:53744200-53752600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr4:53744400-53750600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:53744400-53751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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