Variant report

Variant	rs4235505
Chromosome Location	chr5:179465470-179465471
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	chr5:179463832..179465886-chr5:179496517..179500422,3	MCF-7	breast:
2	chr5:179451853..179453889-chr5:179463627..179465589,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10051632	0.82[AFR][1000 genomes]
rs10051694	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10056316	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10056991	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059400	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10066845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079029	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10464058	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11249663	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249664	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249665	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249666	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739706	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11748441	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11750102	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435998	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681274	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776946	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776948	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4264913	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700859	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57008562	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57117216	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61356660	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62404970	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62404974	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62404976	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404977	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404979	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405015	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601077	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6601078	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869349	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873317	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873639	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729516	0.89[EUR][1000 genomes]
rs7734329	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9329095	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:179447800-179466800	Weak transcription	Hela-S3	cervix
4	chr5:179450600-179466000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:179455800-179467600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:179458800-179467000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:179458800-179467200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:179458800-179468200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:179459400-179467600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:179459600-179467400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:179460400-179467400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:179462000-179467200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:179462400-179467200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:179462400-179467400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:179462400-179467800	Strong transcription	Left Ventricle	heart
18	chr5:179462800-179467200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:179462800-179474800	Weak transcription	Fetal Heart	heart
20	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
21	chr5:179463000-179467400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:179463400-179467200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:179463600-179465600	Weak transcription	NHLF	lung
24	chr5:179463600-179466200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:179463600-179467000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:179463600-179467200	Strong transcription	Liver	Liver
27	chr5:179463600-179467400	Weak transcription	Pancreas	Pancrea
28	chr5:179463600-179467400	Strong transcription	HSMM	muscle
29	chr5:179463600-179467600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:179463600-179467600	Weak transcription	Brain Angular Gyrus	brain
31	chr5:179463600-179467600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:179463600-179467800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:179463600-179467800	Weak transcription	Fetal Thymus	thymus
34	chr5:179463600-179468800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:179463600-179472800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr5:179463600-179473400	Weak transcription	HUVEC	blood vessel
37	chr5:179463600-179475600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:179463800-179467600	Strong transcription	Adipose Nuclei	Adipose
39	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
40	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr5:179464000-179467200	Weak transcription	Fetal Brain Male	brain
43	chr5:179464200-179469000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:179464400-179467200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:179464400-179467400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:179464400-179467800	Strong transcription	Fetal Lung	lung
47	chr5:179464400-179473200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:179464400-179473400	Weak transcription	Spleen	Spleen
49	chr5:179464400-179476800	Weak transcription	HepG2	liver
50	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum

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