Variant report

Variant	rs917977
Chromosome Location	chr2:40321189-40321190
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	chr2:40319121..40321528-chr2:40332638..40334554,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11692733	0.85[ASN][1000 genomes]
rs12151560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614752	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032715	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57918209	0.83[ASN][1000 genomes]
rs6735429	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs917977	PLEKHA4	trans	cerebellum	SCAN
rs917977	HAAO	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40315200-40321800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:40317600-40321800	Weak transcription	Osteobl	bone
3	chr2:40319800-40321200	Enhancers	Fetal Brain Male	brain
4	chr2:40320000-40321400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:40320000-40321600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:40320000-40322800	Enhancers	Fetal Lung	lung
7	chr2:40320000-40325600	Enhancers	HSMMtube	muscle
8	chr2:40320000-40325800	Enhancers	NHLF	lung
9	chr2:40320000-40326600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:40320000-40332200	Enhancers	HSMM	muscle
11	chr2:40320000-40332600	Enhancers	NHDF-Ad	bronchial
12	chr2:40320200-40321200	Enhancers	Fetal Intestine Large	intestine
13	chr2:40320200-40323000	Enhancers	Dnd41	blood
14	chr2:40320200-40325000	Enhancers	Fetal Heart	heart
15	chr2:40320400-40321200	Enhancers	Fetal Brain Female	brain
16	chr2:40320400-40321200	Enhancers	Fetal Intestine Small	intestine
17	chr2:40320400-40321200	Enhancers	Right Ventricle	heart
18	chr2:40320400-40322000	Enhancers	Adipose Nuclei	Adipose
19	chr2:40320400-40322400	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:40320600-40322000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:40320600-40323800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:40320800-40322800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr2:40321000-40321800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:40321000-40322000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:40321000-40322000	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:40321000-40322000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:40321000-40322000	Weak transcription	NH-A	brain
28	chr2:40321000-40326000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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