Variant report

Variant	rs388195
Chromosome Location	chr3:50669765-50669766
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50668689..50671062-chr3:50673046..50675259,2	K562	blood:
2	chr3:50667896..50669989-chr3:50679232..50681112,3	K562	blood:
3	chr3:50668689..50672125-chr3:50673046..50675636,3	K562	blood:
4	chr3:50661810..50665034-chr3:50668635..50670434,3	MCF-7	breast:
5	chr3:50653782..50659891-chr3:50667242..50673193,6	K562	blood:
6	chr3:50653782..50658590-chr3:50669577..50673193,4	K562	blood:
7	chr3:50661088..50664014-chr3:50668534..50670776,2	K562	blood:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1905516	1.00[AMR][1000 genomes]
rs201195	1.00[AMR][1000 genomes]
rs2249775	1.00[AMR][1000 genomes]
rs2355339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2609009	1.00[AMR][1000 genomes]
rs2675780	1.00[AMR][1000 genomes]
rs2675805	1.00[AMR][1000 genomes]
rs414856	1.00[AMR][1000 genomes]
rs4234696	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4688706	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs608961	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446209	0.85[AFR][1000 genomes]
rs6779405	1.00[AMR][1000 genomes]
rs6790086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629126	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7650776	1.00[AMR][1000 genomes]
rs9854316	1.00[AMR][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	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50655400-50677800	Weak transcription	Aorta	Aorta
2	chr3:50655600-50681200	Weak transcription	Fetal Brain Female	brain
3	chr3:50656000-50675600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50656000-50677800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:50660200-50671600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:50660200-50677000	Weak transcription	Liver	Liver
8	chr3:50661400-50671600	Enhancers	Left Ventricle	heart
9	chr3:50661600-50670600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:50661600-50674400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:50661600-50675800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
13	chr3:50662400-50670000	Weak transcription	Fetal Lung	lung
14	chr3:50662400-50671000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:50662400-50672000	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:50662400-50678200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:50662600-50675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:50663200-50677600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:50664200-50672600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:50664400-50672800	Genic enhancers	Dnd41	blood
22	chr3:50665200-50674400	Weak transcription	Colonic Mucosa	Colon
23	chr3:50665400-50671000	Genic enhancers	NHEK	skin
24	chr3:50665400-50671200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:50665400-50679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:50665400-50686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:50665600-50670000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:50665600-50673800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:50665600-50675600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:50665600-50686200	Weak transcription	Stomach Mucosa	stomach
31	chr3:50665800-50669800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:50665800-50670200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:50665800-50670400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:50665800-50670800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:50665800-50671200	Enhancers	HMEC	breast
36	chr3:50665800-50672200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:50665800-50674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:50665800-50675400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:50665800-50675600	Weak transcription	Brain Substantia Nigra	brain
40	chr3:50665800-50675800	Weak transcription	NHLF	lung
41	chr3:50666000-50670000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr3:50666000-50671800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr3:50666200-50669800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:50666200-50671400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:50666200-50673600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:50666600-50675400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:50667000-50674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr3:50667200-50670200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:50667200-50671000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:50667200-50673800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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