Variant report

Variant	rs62405021
Chromosome Location	chr5:179473218-179473219
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179469293..179473403-chr5:179473812..179477504,5	MCF-7	breast:
2	chr5:179466042..179468757-chr5:179469985..179473584,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10051632	0.81[EUR][1000 genomes]
rs10061480	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068039	0.81[EUR][1000 genomes]
rs10068529	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068594	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078977	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10464097	0.81[EUR][1000 genomes]
rs10479455	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10479557	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10903246	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1102190	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12153541	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653944	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12656219	0.83[ASN][1000 genomes]
rs173562	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs185076	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2386704	0.84[ASN][1000 genomes]
rs248257	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs248258	0.88[EUR][1000 genomes]
rs248316	0.87[EUR][1000 genomes]
rs248319	0.81[EUR][1000 genomes]
rs27013	0.88[EUR][1000 genomes]
rs27014	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27016	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs27019	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs394588	0.81[EUR][1000 genomes]
rs4130025	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418384	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4340879	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4466125	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449511	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4700855	0.83[ASN][1000 genomes]
rs55734821	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62405020	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871596	0.81[EUR][1000 genomes]
rs6884290	0.91[ASN][1000 genomes]
rs6888883	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7706570	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs857182	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs857183	0.86[EUR][1000 genomes]
rs857189	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9329096	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179462800-179474800	Weak transcription	Fetal Heart	heart
5	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
6	chr5:179463600-179473400	Weak transcription	HUVEC	blood vessel
7	chr5:179463600-179475600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
9	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:179464400-179473400	Weak transcription	Spleen	Spleen
12	chr5:179464400-179476800	Weak transcription	HepG2	liver
13	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:179464600-179473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:179464600-179473800	Weak transcription	Right Ventricle	heart
16	chr5:179464600-179474400	Weak transcription	Primary T cells from cord blood	blood
17	chr5:179464800-179473800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:179465200-179473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:179465200-179474800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:179465200-179474800	Weak transcription	Psoas Muscle	Psoas
22	chr5:179465200-179475800	Weak transcription	HSMMtube	muscle
23	chr5:179465400-179473400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:179465400-179473400	Weak transcription	Primary B cells from cord blood	blood
25	chr5:179465400-179473600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:179465400-179474600	Weak transcription	Lung	lung
27	chr5:179465400-179477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
29	chr5:179465600-179474800	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:179467400-179474600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:179467400-179474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:179467400-179483200	Weak transcription	HSMM	muscle
33	chr5:179467600-179473600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:179467600-179473600	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:179467600-179474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:179467600-179474800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:179467800-179473400	Weak transcription	Fetal Lung	lung
38	chr5:179467800-179474800	Weak transcription	Left Ventricle	heart
39	chr5:179467800-179474800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:179467800-179475800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:179467800-179479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:179468000-179473400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:179468000-179474800	Weak transcription	Liver	Liver
44	chr5:179468200-179473400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:179468200-179477400	Weak transcription	A549	lung
46	chr5:179468600-179473600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:179468800-179475600	Weak transcription	Gastric	stomach
48	chr5:179469000-179477000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:179470600-179475600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr5:179470800-179473400	Weak transcription	Brain Angular Gyrus	brain

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