Variant report

Variant	rs59834324
Chromosome Location	chr6:28552123-28552124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28551138-28552209	K562	blood:	n/a	n/a
2	GATA3	chr6:28552101-28552294	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28551064..28553873-chr7:151215721..151217781,2	MCF-7	breast:
2	chr6:28548777..28553647-chr6:28554633..28557663,4	K562	blood:
3	chr6:28551519..28553325-chr6:28583794..28585508,2	K562	blood:
4	chr6:28550071..28553213-chr6:28554633..28557034,4	K562	blood:

Variant related genes	Relation type
ENSG00000246350	TF binding region
ENSG00000246350	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000106615	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs16894180	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16894183	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16894218	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34626566	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35783771	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4441948	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55826226	1.00[AMR][1000 genomes]
rs55906309	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56100858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56127972	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56208653	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56364512	1.00[AMR][1000 genomes]
rs56958472	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57672617	1.00[AMR][1000 genomes]
rs58172306	1.00[AMR][1000 genomes]
rs58341861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59109668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60661227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740605	1.00[AMR][1000 genomes]
rs73740628	1.00[AMR][1000 genomes]
rs73740636	1.00[AMR][1000 genomes]
rs73740738	1.00[AMR][1000 genomes]
rs73740740	1.00[AMR][1000 genomes]
rs73740741	1.00[AMR][1000 genomes]
rs73740742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740747	0.94[AFR][1000 genomes]
rs73740968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742927	1.00[AMR][1000 genomes]
rs73742928	1.00[AMR][1000 genomes]
rs73742929	1.00[AMR][1000 genomes]
rs73742930	1.00[AMR][1000 genomes]
rs73742931	1.00[AMR][1000 genomes]
rs73742932	1.00[AMR][1000 genomes]
rs73743506	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73743507	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73743508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73743510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73743511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73744130	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73744134	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73744135	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73744136	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73744140	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73744141	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs963937	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28531800-28553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28532000-28552600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:28535000-28554000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:28536600-28553200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:28537200-28553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:28538800-28553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28539400-28552800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:28540000-28554000	Weak transcription	Gastric	stomach
11	chr6:28540600-28554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:28541000-28554200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:28541400-28553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:28541400-28554000	Weak transcription	Pancreas	Pancrea
15	chr6:28542200-28553200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:28542600-28553000	Weak transcription	Fetal Intestine Small	intestine
17	chr6:28543600-28552400	Weak transcription	HepG2	liver
18	chr6:28543800-28553000	Weak transcription	Fetal Kidney	kidney
19	chr6:28543800-28553200	Weak transcription	Liver	Liver
20	chr6:28544000-28553200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:28544200-28552400	Weak transcription	Brain Germinal Matrix	brain
22	chr6:28544600-28552200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:28546200-28553000	Weak transcription	HMEC	breast
24	chr6:28548000-28554000	Weak transcription	Right Atrium	heart
25	chr6:28548200-28554000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:28550600-28554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:28551000-28554000	Weak transcription	Right Ventricle	heart
28	chr6:28551400-28552200	Enhancers	Fetal Brain Female	brain
29	chr6:28551600-28554000	Enhancers	Fetal Lung	lung
30	chr6:28551800-28552400	Weak transcription	K562	blood
31	chr6:28551800-28552800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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