Variant report

Variant	rs6542080
Chromosome Location	chr2:113464495-113464496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113460336..113462064-chr2:113462698..113465234,2	MCF-7	breast:
2	chr2:113340714..113343330-chr2:113462470..113465365,2	K562	blood:
3	chr2:113440346..113442226-chr2:113462249..113464616,2	K562	blood:
4	chr2:113456909..113459689-chr2:113463239..113465215,3	K562	blood:
5	chr2:113382749..113384471-chr2:113464194..113466806,2	K562	blood:
6	chr2:113398028..113400267-chr2:113464007..113465534,2	K562	blood:
7	chr2:113463436..113465065-chr2:113468008..113469803,2	K562	blood:
8	chr2:113448136..113451389-chr2:113461614..113465494,4	K562	blood:
9	chr2:113463027..113465747-chr2:113466375..113467999,2	K562	blood:
10	chr2:113448771..113451782-chr2:113462370..113466299,3	K562	blood:
11	chr2:113458059..113460940-chr2:113462365..113464957,4	K562	blood:
12	chr2:113385104..113391547-chr2:113463938..113470179,6	K562	blood:
13	chr2:113462515..113465478-chr2:113468024..113470345,2	K562	blood:
14	chr2:113462767..113464610-chr2:113470290..113471852,2	K562	blood:
15	chr2:113461776..113469381-chr2:113473397..113480932,10	K562	blood:
16	chr2:113407931..113409765-chr2:113463471..113465338,2	K562	blood:
17	chr2:113401060..113404507-chr2:113463358..113467021,5	K562	blood:
18	chr2:113401472..113405460-chr2:113462823..113466044,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000144136	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10173049	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10174076	0.91[ASN][1000 genomes]
rs1018317	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201756	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10211073	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11692751	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222131	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848291	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848292	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848293	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848295	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4849106	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849107	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542077	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542078	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542079	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542081	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542082	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73955258	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567215	0.97[AMR][1000 genomes];0.99[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	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv526301	chr2:113451498-113495785	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3458160	chr2:113460280-113484749	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3458161	chr2:113460322-113484724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv3458162	chr2:113460460-113484652	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv441775	chr2:113462399-113478887	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6542080	SLC20A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113458800-113469000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr2:113462000-113468800	Enhancers	Primary hematopoietic stem cells	blood
3	chr2:113462400-113465600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:113462600-113469400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:113462800-113465400	Enhancers	HMEC	breast
6	chr2:113462800-113469200	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:113463000-113465800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:113463000-113469000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:113463200-113464600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:113463200-113465000	Enhancers	Fetal Thymus	thymus
11	chr2:113463200-113465200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr2:113463200-113465400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:113463200-113465400	Enhancers	NHEK	skin
14	chr2:113463200-113465800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:113463200-113467000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:113463400-113464600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:113463400-113465400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:113463400-113465400	Enhancers	Primary B cells from cord blood	blood
19	chr2:113463400-113465600	Flanking Active TSS	GM12878-XiMat	blood
20	chr2:113463400-113467000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr2:113463400-113467600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:113464000-113464600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:113464000-113465400	Enhancers	Dnd41	blood
24	chr2:113464200-113465000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:113464200-113465000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr2:113464200-113465200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:113464200-113467200	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:113464200-113486400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:113464400-113464800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:113464400-113464800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:113464400-113464800	Weak transcription	Spleen	Spleen
32	chr2:113464400-113465000	Enhancers	K562	blood
33	chr2:113464400-113465400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:113464400-113466600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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