Variant report

Variant	rs316224
Chromosome Location	chr5:96414272-96414273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96413541..96415661-chr5:96445428..96448359,2	MCF-7	breast:
2	chr5:96405505..96407862-chr5:96413976..96415782,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10039917	0.84[ASN][1000 genomes]
rs10043135	0.85[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10071737	0.82[ASN][1000 genomes]
rs1035507	0.84[ASN][1000 genomes]
rs10463198	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11748432	0.84[ASN][1000 genomes]
rs11954059	0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12110061	0.84[ASN][1000 genomes]
rs12520374	0.80[ASN][1000 genomes]
rs13167790	0.81[ASN][1000 genomes]
rs182625	0.87[ASN][1000 genomes]
rs186413	0.81[ASN][1000 genomes]
rs2287903	0.84[ASN][1000 genomes]
rs2544769	0.80[CHB][hapmap]
rs2544776	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316178	0.82[ASN][1000 genomes]
rs316190	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs316201	0.85[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs316202	0.81[ASN][1000 genomes]
rs316203	0.81[ASN][1000 genomes]
rs316204	0.81[ASN][1000 genomes]
rs316205	0.81[ASN][1000 genomes]
rs316207	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs316209	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs316213	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs316217	0.84[ASN][1000 genomes]
rs316218	0.83[ASN][1000 genomes]
rs316219	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs316220	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[TSI][hapmap]
rs316223	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316232	0.87[ASN][1000 genomes]
rs316233	0.85[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.87[ASN][1000 genomes]
rs316234	0.85[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs389536	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392723	0.95[ASN][1000 genomes]
rs444243	0.83[ASN][1000 genomes]
rs6556945	0.88[ASN][1000 genomes]
rs7717829	0.85[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	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv4924	chr5:96391451-96437233	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs316224	LIX1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96411000-96414600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr5:96411400-96417600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:96411800-96414600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:96412000-96414600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:96414000-96416000	Enhancers	Primary B cells from cord blood	blood
6	chr5:96414200-96414400	Enhancers	Fetal Heart	heart
7	chr5:96414200-96415600	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:96414200-96415800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:96414200-96417400	Enhancers	Monocytes-CD14+_RO01746	blood

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