Variant report

Variant	rs316233
Chromosome Location	chr5:96427624-96427625
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96425190..96428341-chr5:96429686..96433552,4	K562	blood:

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

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

rs_ID	r²[population]
rs10039917	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10043135	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10071737	0.92[ASN][1000 genomes]
rs1035507	0.94[ASN][1000 genomes]
rs10463198	0.85[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs11954059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11958159	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs12520374	0.90[ASN][1000 genomes]
rs13167790	0.91[ASN][1000 genomes]
rs182625	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287903	0.94[ASN][1000 genomes]
rs2544769	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2544776	0.85[ASN][1000 genomes]
rs316178	0.92[ASN][1000 genomes]
rs316190	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316201	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs316202	0.90[ASN][1000 genomes]
rs316203	0.91[ASN][1000 genomes]
rs316204	0.91[ASN][1000 genomes]
rs316205	0.91[ASN][1000 genomes]
rs316207	0.89[CHD][hapmap]
rs316209	0.89[CHD][hapmap];0.84[JPT][hapmap]
rs316213	0.85[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs316217	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs316218	0.93[ASN][1000 genomes]
rs316219	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs316222	0.82[AMR][1000 genomes]
rs316223	0.84[ASN][1000 genomes]
rs316224	0.87[ASN][1000 genomes]
rs316232	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316234	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389536	0.85[ASN][1000 genomes]
rs392723	0.82[ASN][1000 genomes]
rs444243	0.93[ASN][1000 genomes]
rs6556945	0.88[ASN][1000 genomes]
rs7717829	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	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
4	nsv969966	chr5:96418895-96427787	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs316233	LIX1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96423200-96430200	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:96425200-96437000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:96425400-96428200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:96425600-96430200	Weak transcription	Primary B cells from cord blood	blood
5	chr5:96425600-96430600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:96425800-96430600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr5:96426400-96437200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:96426600-96427800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:96426800-96430200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:96427000-96428800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:96427000-96430200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:96427400-96428400	Enhancers	K562	blood
13	chr5:96427400-96429200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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