Variant report

Variant	rs62386590
Chromosome Location	chr6:4836889-4836890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4775417..4779410-chr6:4834974..4837006,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1016877	0.85[EUR][1000 genomes]
rs11967994	0.80[EUR][1000 genomes]
rs11968021	0.81[EUR][1000 genomes]
rs1265332	0.83[EUR][1000 genomes]
rs1265333	0.83[EUR][1000 genomes]
rs1265334	0.81[EUR][1000 genomes]
rs1265335	0.81[EUR][1000 genomes]
rs17138856	0.83[EUR][1000 genomes]
rs184588	0.81[EUR][1000 genomes]
rs2179269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179270	0.83[EUR][1000 genomes]
rs233476	0.81[EUR][1000 genomes]
rs3748078	0.87[EUR][1000 genomes]
rs61610972	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62384662	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62384663	0.84[AMR][1000 genomes]
rs62386571	0.86[ASN][1000 genomes]
rs62386574	0.81[EUR][1000 genomes]
rs62386575	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62386576	0.83[EUR][1000 genomes]
rs62386577	0.83[EUR][1000 genomes]
rs62386578	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62386582	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386584	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386585	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386587	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386591	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386593	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386594	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386612	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386614	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910368	0.91[EUR][1000 genomes]
rs6918626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6924037	0.89[AMR][1000 genomes]
rs73362560	0.83[EUR][1000 genomes]
rs808608	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378917	0.84[AMR][1000 genomes]
rs9378919	0.89[AMR][1000 genomes]
rs9392640	0.89[AMR][1000 genomes]
rs9405786	0.89[AMR][1000 genomes]
rs9504254	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv966675	chr6:4819733-4855009	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4820400-4844200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4821200-4853600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:4830000-4838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:4830000-4840600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:4830000-4848800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:4830200-4837000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:4830800-4844200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:4835200-4844200	Weak transcription	NHEK	skin
9	chr6:4835600-4837000	Weak transcription	K562	blood
10	chr6:4836200-4837000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:4836200-4844600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:4836400-4837200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:4836400-4837200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
14	chr6:4836400-4837600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
15	chr6:4836400-4837600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:4836400-4837600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:4836400-4837600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr6:4836600-4837200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr6:4836600-4837400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr6:4836600-4837400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr6:4836600-4837400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:4836600-4837400	Flanking Active TSS	Hela-S3	cervix
23	chr6:4836600-4838400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:4836800-4837200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
25	chr6:4836800-4837400	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr6:4836800-4837400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
27	chr6:4836800-4837600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr6:4836800-4848600	Weak transcription	Right Ventricle	heart

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