Variant report

Variant	rs1428012
Chromosome Location	chr5:5178945-5178946
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	chr5:5177669..5180666-chr5:5181916..5184715,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10036706	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10040074	0.80[AMR][1000 genomes]
rs4701693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702234	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021653	chr5:4932992-5201887	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2757980	chr5:4980876-5184615	Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2759318	chr5:4980876-5184615	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv830194	chr5:5002459-5187667	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1428012	IRX1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5176000-5180400	Enhancers	Fetal Kidney	kidney
2	chr5:5176200-5181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:5176400-5179200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:5176400-5179800	Weak transcription	Pancreas	Pancrea
5	chr5:5177200-5179000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr5:5177200-5179200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:5177200-5179400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr5:5177200-5179400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:5177200-5181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:5177600-5179000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:5177600-5183200	Weak transcription	Gastric	stomach
12	chr5:5177600-5185000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:5177800-5179400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:5178200-5179000	Enhancers	Liver	Liver
15	chr5:5178200-5179000	Enhancers	HepG2	liver
16	chr5:5178200-5179400	Enhancers	Fetal Lung	lung
17	chr5:5178200-5181000	Enhancers	NH-A	brain
18	chr5:5178400-5179000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:5178400-5179000	Enhancers	Ovary	ovary
20	chr5:5178600-5179800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:5178800-5179000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:5178800-5179000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr5:5178800-5179200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:5178800-5180000	Enhancers	A549	lung
25	chr5:5178800-5180400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:5178800-5180600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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