Variant report

Variant	rs56990501
Chromosome Location	chr3:52050340-52050341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52049402..52051939-chr3:52063118..52065044,2	K562	blood:
2	chr3:52048430..52050656-chr3:52053899..52056295,3	K562	blood:
3	chr3:52048055..52051356-chr3:52052467..52056276,3	K562	blood:
4	chr3:52047829..52051177-chr3:52089052..52092648,3	MCF-7	breast:
5	chr3:52048651..52051946-chr3:52056389..52059628,4	K562	blood:
6	chr3:52048651..52051918-chr3:52057028..52059628,3	K562	blood:
7	chr3:52050186..52052732-chr3:52065532..52068368,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164086	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11130297	1.00[EUR][1000 genomes]
rs1587921	1.00[EUR][1000 genomes]
rs17052020	1.00[EUR][1000 genomes]
rs5743838	1.00[EUR][1000 genomes]
rs60643756	1.00[EUR][1000 genomes]
rs6445259	1.00[EUR][1000 genomes]
rs6775662	1.00[EUR][1000 genomes]
rs6782809	1.00[EUR][1000 genomes]
rs6784563	1.00[EUR][1000 genomes]
rs6784653	1.00[EUR][1000 genomes]
rs6797786	1.00[EUR][1000 genomes]
rs7614535	1.00[EUR][1000 genomes]
rs7617023	1.00[EUR][1000 genomes]
rs7623076	1.00[EUR][1000 genomes]
rs7625515	1.00[EUR][1000 genomes]
rs7636412	1.00[EUR][1000 genomes]
rs7652984	1.00[EUR][1000 genomes]
rs973948	1.00[EUR][1000 genomes]
rs973949	1.00[EUR][1000 genomes]
rs9860132	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
11	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52040800-52056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:52041000-52050400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:52046200-52058600	Enhancers	Spleen	Spleen
4	chr3:52046200-52060600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:52046600-52052000	Enhancers	Placenta	Placenta
6	chr3:52046800-52055400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:52047200-52050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:52047400-52051800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:52047600-52051800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:52048000-52056600	Enhancers	Right Ventricle	heart
11	chr3:52048600-52050800	Enhancers	Fetal Heart	heart
12	chr3:52048600-52051000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52048600-52056600	Enhancers	Left Ventricle	heart
14	chr3:52048600-52056800	Enhancers	Psoas Muscle	Psoas
15	chr3:52048600-52061000	Enhancers	Fetal Muscle Leg	muscle
16	chr3:52048800-52051800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:52049000-52050800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52049200-52052800	Weak transcription	Brain Anterior Caudate	brain
19	chr3:52049200-52055800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:52049400-52053600	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:52049800-52050800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:52049800-52051200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:52049800-52053400	Weak transcription	K562	blood
24	chr3:52049800-52053600	Weak transcription	GM12878-XiMat	blood
25	chr3:52049800-52055200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:52050000-52055600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:52050000-52056600	Enhancers	Right Atrium	heart
28	chr3:52050200-52050600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr3:52050200-52050800	Enhancers	Lung	lung
30	chr3:52050200-52051400	Enhancers	Brain Angular Gyrus	brain
31	chr3:52050200-52052000	Enhancers	Brain Cingulate Gyrus	brain
32	chr3:52050200-52052000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:52050200-52052600	Enhancers	Stomach Smooth Muscle	stomach
34	chr3:52050200-52053200	Weak transcription	Fetal Intestine Small	intestine

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