Variant report

Variant	rs301135
Chromosome Location	chr4:53778384-53778385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53777529..53778533-chr4:53845044..53845617,3	MCF-7	breast:
2	chr4:53777687..53778479-chr5:44332371..44332986,2	MCF-7	breast:
3	chr4:53770183..53772552-chr4:53775359..53778857,3	MCF-7	breast:
4	chr4:53771606..53774291-chr4:53776338..53779247,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10001855	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10008073	0.80[AMR][1000 genomes]
rs10014464	0.80[AMR][1000 genomes]
rs1043975	0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs1047959	0.85[JPT][hapmap]
rs10866413	0.89[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs11934293	0.80[AMR][1000 genomes]
rs11941562	0.83[AMR][1000 genomes]
rs1483685	0.80[AMR][1000 genomes]
rs1483686	0.83[TSI][hapmap]
rs17082081	0.80[AMR][1000 genomes]
rs17082143	0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17082147	0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17643154	0.87[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1963003	0.80[AMR][1000 genomes]
rs2017237	0.85[JPT][hapmap]
rs2062253	0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs2279334	0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs2306601	0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2411259	0.83[TSI][hapmap]
rs28419463	0.80[AMR][1000 genomes]
rs28704139	0.80[AMR][1000 genomes]
rs2898681	0.85[JPT][hapmap]
rs301090	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs301097	0.84[YRI][hapmap]
rs301117	0.83[ASN][1000 genomes]
rs301118	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs301119	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs301120	0.84[ASN][1000 genomes]
rs301121	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs301122	0.85[ASN][1000 genomes]
rs301123	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs301124	0.85[ASN][1000 genomes]
rs301126	0.88[YRI][hapmap]
rs301131	0.88[YRI][hapmap]
rs301136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs448567	0.92[YRI][hapmap]
rs4864679	0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs4864681	0.83[AMR][1000 genomes]
rs4864682	0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs4864683	0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs4864691	0.85[JPT][hapmap]
rs5012592	0.83[TSI][hapmap]
rs62336785	0.80[AMR][1000 genomes]
rs62336791	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62336792	0.83[AMR][1000 genomes]
rs62336794	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62336823	0.80[ASN][1000 genomes]
rs6839084	0.85[JPT][hapmap]
rs6852148	0.85[JPT][hapmap]
rs73143042	0.80[AMR][1000 genomes]
rs7654682	0.81[AMR][1000 genomes]
rs90020	0.88[YRI][hapmap]
rs900607	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs922932	0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs922933	0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs9646	0.80[AMR][1000 genomes]
rs9993034	0.83[AMR][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	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
2	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:53736600-53785600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:53737200-53779200	Weak transcription	Gastric	stomach
5	chr4:53757000-53781200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:53761000-53788000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:53766600-53780600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:53767600-53789000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:53767800-53782000	Weak transcription	Aorta	Aorta
10	chr4:53768000-53782000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:53768200-53779000	Weak transcription	Ovary	ovary
12	chr4:53768200-53779800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:53768400-53779000	Weak transcription	Liver	Liver
14	chr4:53768400-53779000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:53768400-53782000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:53768600-53788200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:53768800-53815600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:53769000-53804400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:53769400-53782000	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:53769600-53779800	Weak transcription	Fetal Lung	lung
21	chr4:53769600-53785000	Weak transcription	Primary B cells from cord blood	blood
22	chr4:53769600-53792000	Weak transcription	Lung	lung
23	chr4:53770600-53779200	Weak transcription	Left Ventricle	heart
24	chr4:53770600-53780200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:53770800-53781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:53771000-53791600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:53771200-53778800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:53771200-53780000	Weak transcription	NH-A	brain
29	chr4:53771200-53780600	Weak transcription	HSMM	muscle
30	chr4:53771400-53779000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:53771600-53780200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:53772400-53781800	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:53773600-53787000	Weak transcription	Dnd41	blood
34	chr4:53773800-53784800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:53774400-53779000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:53774600-53778600	Weak transcription	Fetal Heart	heart
37	chr4:53774600-53778800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:53774600-53798400	Weak transcription	HSMMtube	muscle
39	chr4:53774800-53779000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:53774800-53779000	Weak transcription	Osteobl	bone
41	chr4:53774800-53779400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:53774800-53779400	Weak transcription	NHLF	lung
43	chr4:53774800-53780600	Weak transcription	Fetal Stomach	stomach
44	chr4:53774800-53783600	Weak transcription	Primary T cells from cord blood	blood
45	chr4:53775800-53779200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:53778000-53778400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr4:53778000-53778400	Enhancers	NHEK	skin
48	chr4:53778000-53780400	Enhancers	Stomach Mucosa	stomach
49	chr4:53778000-53782200	Enhancers	Pancreas	Pancrea
50	chr4:53778000-53783000	Enhancers	NHDF-Ad	bronchial

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