Variant report

Variant	rs6427300
Chromosome Location	chr1:153805677-153805678
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153803578..153805707-chr1:153809227..153810744,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10908525	0.87[AFR][1000 genomes]
rs11264573	0.83[EUR][1000 genomes]
rs11264736	0.81[AFR][1000 genomes]
rs1127091	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1139620	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800001	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12120118	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124424	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129468	0.93[ASN][1000 genomes]
rs12130611	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133492	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133923	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12142639	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142733	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12738361	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252508	0.85[AFR][1000 genomes]
rs35711150	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4276953	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370789	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4451582	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4540690	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581307	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596938	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803655	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427306	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668066	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677794	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6690619	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6700115	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72694233	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414227	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7415004	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7522030	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7532974	0.83[AFR][1000 genomes]
rs7554469	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426935	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426938	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427232	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427233	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	esv1830663	chr1:153779296-153807816	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	esv1825546	chr1:153779296-153821716	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153778400-153820400	Weak transcription	Stomach Mucosa	stomach
2	chr1:153781600-153826800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:153786400-153811000	Weak transcription	Psoas Muscle	Psoas
4	chr1:153790200-153814400	Weak transcription	Small Intestine	intestine
5	chr1:153791600-153822200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:153791800-153845600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:153792000-153822000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:153798400-153814200	Weak transcription	NHDF-Ad	bronchial
9	chr1:153799200-153811000	Weak transcription	Right Atrium	heart
10	chr1:153800000-153824400	Weak transcription	Brain Germinal Matrix	brain
11	chr1:153800600-153814000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:153800600-153824600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:153800800-153805800	Weak transcription	Liver	Liver
14	chr1:153800800-153806000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:153800800-153807200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:153800800-153807200	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:153800800-153810200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:153800800-153813000	Weak transcription	GM12878-XiMat	blood
19	chr1:153800800-153813800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:153800800-153814400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:153800800-153814400	Weak transcription	NH-A	brain
22	chr1:153800800-153815800	Weak transcription	Right Ventricle	heart
23	chr1:153800800-153816000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:153800800-153816200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:153800800-153816400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:153800800-153818200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:153800800-153818600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:153800800-153821000	Weak transcription	Gastric	stomach
29	chr1:153800800-153821400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:153800800-153822600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:153800800-153823600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:153800800-153823800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:153800800-153824200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:153800800-153824400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:153800800-153824400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:153800800-153824400	Weak transcription	Fetal Intestine Large	intestine
37	chr1:153800800-153824800	Weak transcription	Fetal Lung	lung
38	chr1:153800800-153825000	Weak transcription	HSMM	muscle
39	chr1:153800800-153825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:153800800-153825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:153800800-153825400	Weak transcription	Pancreas	Pancrea
42	chr1:153800800-153827000	Weak transcription	HUVEC	blood vessel
43	chr1:153800800-153830800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:153800800-153832600	Weak transcription	Aorta	Aorta
45	chr1:153800800-153832800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:153800800-153835600	Weak transcription	Ovary	ovary
47	chr1:153800800-153850800	Weak transcription	A549	lung
48	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
49	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
50	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart

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