Variant report

Variant	rs4916829
Chromosome Location	chr5:90195447-90195448
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90194213..90195845-chr5:90213067..90215905,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10044202	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045071	1.00[CHB][hapmap]
rs10052015	0.83[CHB][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053303	0.83[CHB][hapmap]
rs10059629	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs10060641	0.83[CHB][hapmap];0.93[CHD][hapmap];0.80[TSI][hapmap]
rs10061193	0.99[ASN][1000 genomes]
rs10078496	0.83[CHB][hapmap]
rs10474336	0.92[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10514339	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs12054681	0.83[CHB][hapmap];0.93[CHD][hapmap];0.83[TSI][hapmap]
rs12513628	0.81[ASN][1000 genomes]
rs12520956	0.83[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12522395	0.92[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs16869175	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2247415	0.92[CHB][hapmap]
rs2366935	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2438338	1.00[CHB][hapmap]
rs2438342	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2438343	0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs2438344	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2438345	0.83[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs2438351	0.92[CHB][hapmap]
rs2438353	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs2443068	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]
rs28437109	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098356	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4916698	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs4916826	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4916827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916828	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57107124	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6878896	0.83[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
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
rs4916829	LOC645323	cis	parietal	SCAN
rs4916829	LOC645323	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90185000-90226600	Weak transcription	K562	blood
2	chr5:90186400-90218000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90192800-90204400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:90192800-90204800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:90193800-90195600	Weak transcription	Gastric	stomach
6	chr5:90193800-90195800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr5:90194000-90195800	Enhancers	Duodenum Mucosa	Duodenum
8	chr5:90194200-90198400	Enhancers	Fetal Intestine Small	intestine
9	chr5:90194400-90195800	Enhancers	Pancreas	Pancrea
10	chr5:90194400-90195800	Enhancers	Stomach Mucosa	stomach
11	chr5:90194400-90198400	Enhancers	Fetal Intestine Large	intestine
12	chr5:90194600-90195800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:90195000-90195800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:90195000-90195800	Flanking Active TSS	Liver	Liver
15	chr5:90195000-90195800	Flanking Active TSS	HepG2	liver
16	chr5:90195200-90195800	Enhancers	Esophagus	oesophagus
17	chr5:90195400-90196600	Enhancers	A549	lung

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