Variant report

Variant	rs11579490
Chromosome Location	chr1:222050467-222050468
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221915847..221918268-chr1:222049176..222051061,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10746414	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10863657	1.00[ASN][1000 genomes]
rs11118874	1.00[ASN][1000 genomes]
rs11118875	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11118883	1.00[CHB][hapmap]
rs11577023	1.00[CHB][hapmap]
rs11582814	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12083393	1.00[ASN][1000 genomes]
rs12089785	1.00[ASN][1000 genomes]
rs12090948	1.00[ASN][1000 genomes]
rs12095068	1.00[ASN][1000 genomes]
rs12118052	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125690	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12130910	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35090621	0.84[AMR][1000 genomes]
rs4384245	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4528124	0.81[GIH][hapmap]
rs4581289	1.00[ASN][1000 genomes]
rs56010022	1.00[ASN][1000 genomes]
rs6604675	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6604676	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6604677	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658977	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659311	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668784	1.00[ASN][1000 genomes]
rs66698149	1.00[ASN][1000 genomes]
rs6691170	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699132	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67087803	1.00[ASN][1000 genomes]
rs67220535	1.00[ASN][1000 genomes]
rs7544478	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7550628	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556214	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556228	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11579490	HHIPL2	cis	cerebellum	SCAN
rs11579490	AIDA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222043200-222052800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:222043400-222051400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:222043400-222052600	Weak transcription	HSMMtube	muscle
4	chr1:222047800-222054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:222048000-222051400	Weak transcription	HMEC	breast
6	chr1:222048200-222050600	Weak transcription	GM12878-XiMat	blood
7	chr1:222048200-222051400	Weak transcription	Osteobl	bone
8	chr1:222048200-222052000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:222048200-222052400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:222048400-222050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:222048400-222051400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:222048400-222051600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:222048600-222051400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:222048600-222051400	Weak transcription	HSMM	muscle
15	chr1:222048600-222051400	Weak transcription	NH-A	brain
16	chr1:222048600-222051800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:222048600-222051800	Weak transcription	NHLF	lung
18	chr1:222048600-222073600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:222048800-222060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:222049800-222050600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:222049800-222052800	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:222050000-222052600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:222050200-222051000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr1:222050200-222053000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:222050400-222050600	Enhancers	NHDF-Ad	bronchial
26	chr1:222050400-222054000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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