Variant report

Variant	rs6542077
Chromosome Location	chr2:113461941-113461942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113460336..113462064-chr2:113462698..113465234,2	MCF-7	breast:
2	chr2:113415901..113418614-chr2:113461672..113464047,2	K562	blood:
3	chr2:113403381..113406309-chr2:113461047..113462788,2	K562	blood:
4	chr2:113453857..113455888-chr2:113460947..113463917,2	K562	blood:
5	chr2:113448136..113451389-chr2:113461614..113465494,4	K562	blood:
6	chr2:113461776..113469381-chr2:113473397..113480932,10	K562	blood:

Variant related genes	Relation type
ENSG00000144136	Chromatin interaction
ENSG00000144130	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10173049	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10174076	0.89[ASN][1000 genomes]
rs1018317	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201756	0.91[ASN][1000 genomes]
rs10211073	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11692751	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2222131	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4848291	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4848292	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4848293	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4848294	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4848295	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4848296	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849106	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849107	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542078	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6542079	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542081	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542082	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73955258	0.93[ASN][1000 genomes]
rs7567215	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6542077	SLC20A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113451800-113462800	Weak transcription	Dnd41	blood
2	chr2:113458600-113463400	Weak transcription	Osteobl	bone
3	chr2:113458600-113464000	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:113458800-113463400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:113458800-113469000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr2:113459400-113463400	Weak transcription	Primary B cells from cord blood	blood
7	chr2:113459600-113463000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:113459600-113463200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:113459800-113463600	Weak transcription	NHLF	lung
10	chr2:113460000-113462000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:113460000-113462400	Weak transcription	K562	blood
12	chr2:113460000-113463000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:113460200-113462000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:113460200-113462600	Weak transcription	GM12878-XiMat	blood
15	chr2:113460200-113462800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:113460600-113462600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:113460800-113462800	Weak transcription	Monocytes-CD14+_RO01746	blood

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