Variant report

Variant	rs2443068
Chromosome Location	chr5:90182824-90182825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90178610..90180620-chr5:90180935..90182990,2	MCF-7	breast:
2	chr5:90181377..90185761-chr5:90673383..90677784,5	K562	blood:
3	chr5:90180905..90184179-chr5:90184592..90187757,3	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10044202	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10045071	1.00[CHB][hapmap]
rs10052015	0.83[CHB][hapmap]
rs10053303	0.83[CHB][hapmap]
rs10059629	0.92[CHB][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs10060641	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10061193	0.86[ASN][1000 genomes]
rs10078496	0.83[CHB][hapmap]
rs10474336	0.92[CHB][hapmap]
rs10514339	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs12054681	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs12520956	0.83[CHB][hapmap]
rs12522395	0.92[CHB][hapmap];0.86[CHD][hapmap]
rs13159353	0.85[ASN][1000 genomes]
rs16869175	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2247415	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2366935	0.91[CHB][hapmap];0.96[ASN][1000 genomes]
rs2438338	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2438342	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2438343	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs2438344	0.92[CHB][hapmap];0.94[ASN][1000 genomes]
rs2438345	0.83[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs2438351	0.92[CHB][hapmap]
rs2438353	0.92[CHB][hapmap];0.81[CHD][hapmap]
rs28437109	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3098356	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[ASN][1000 genomes]
rs4916698	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs4916826	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916827	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4916828	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4916829	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57107124	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6865577	0.87[ASN][1000 genomes]
rs6878896	0.83[CHB][hapmap]
rs7724016	0.83[CHB][hapmap]
rs881289	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv2754394	chr5:90181320-90225796	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2443068	LOC645323	cis	parietal	SCAN
rs2443068	LOC645323	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90163600-90194400	Weak transcription	Pancreas	Pancrea
2	chr5:90165400-90188800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:90168200-90186000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:90172600-90184400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:90174600-90185600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:90174800-90183400	Weak transcription	Liver	Liver
7	chr5:90175000-90184400	Weak transcription	K562	blood
8	chr5:90179600-90190200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:90179800-90183000	Weak transcription	Esophagus	oesophagus
10	chr5:90179800-90184600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:90179800-90184600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:90179800-90184600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:90179800-90191600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:90179800-90192000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:90180000-90184800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:90180000-90184800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:90180600-90186600	Enhancers	Hela-S3	cervix
18	chr5:90180800-90183000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:90180800-90190200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:90181400-90183200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:90181400-90185400	Enhancers	NHEK	skin
22	chr5:90182800-90183200	Enhancers	Gastric	stomach
23	chr5:90182800-90183800	Enhancers	Stomach Mucosa	stomach
24	chr5:90182800-90184600	Enhancers	A549	lung

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