Variant report

Variant	rs189296
Chromosome Location	chr5:111869675-111869676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:111496398..111498686-chr5:111868058..111870036,2	MCF-7	breast:
2	chr5:111868244..111870833-chr5:111871300..111873976,2	K562	blood:
3	chr5:111868244..111870833-chr5:111871300..111873976,3	K562	blood:

Variant related genes	Relation type
ENSG00000238363	Chromatin interaction
ENSG00000224032	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs163449	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs163451	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163452	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163453	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255703	0.81[EUR][1000 genomes]
rs255706	0.83[EUR][1000 genomes]
rs338845	0.82[ASN][1000 genomes]
rs338847	0.82[ASN][1000 genomes]
rs338855	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424258	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv882715	chr5:111836278-111894491	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
3	nsv882716	chr5:111848890-111894491	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs189296	EPB41L4A	cis	parietal	SCAN
rs189296	DCP2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111865600-111869800	Weak transcription	K562	blood
2	chr5:111867800-111870800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:111868000-111870400	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr5:111868200-111869800	Enhancers	Primary B cells from cord blood	blood
5	chr5:111868200-111870000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:111868200-111870200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:111868400-111870200	Enhancers	Spleen	Spleen
8	chr5:111868400-111870400	Enhancers	Adipose Nuclei	Adipose
9	chr5:111868600-111871200	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:111868800-111871200	Enhancers	Stomach Mucosa	stomach
11	chr5:111869000-111870000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:111869000-111870000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:111869000-111870000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr5:111869000-111870200	Enhancers	Gastric	stomach
15	chr5:111869200-111869800	Enhancers	A549	lung
16	chr5:111869200-111870000	Enhancers	Brain Anterior Caudate	brain
17	chr5:111869200-111870200	Enhancers	Esophagus	oesophagus
18	chr5:111869200-111870200	Enhancers	Pancreas	Pancrea
19	chr5:111869400-111870000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:111869400-111870400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr5:111869400-111870400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr5:111869400-111871000	Enhancers	GM12878-XiMat	blood
23	chr5:111869600-111869800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:111869600-111870000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr5:111869600-111870000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:111869600-111870000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:111869600-111871600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr5:111869600-111880000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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