Variant report

Variant	rs233046
Chromosome Location	chr1:85829405-85829406
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	chr1:85823950..85826978-chr1:85828513..85831070,3	K562	blood:
2	chr1:85827968..85830581-chr1:85830852..85832881,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10782548	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11587876	0.92[CHD][hapmap]
rs17127710	0.81[ASN][1000 genomes]
rs233051	0.81[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233080	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233087	0.95[ASN][1000 genomes]
rs233111	0.87[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233128	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34278923	0.84[ASN][1000 genomes]
rs591917	0.95[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs648216	0.95[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs7532508	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs233046	PKN2	cis	parietal	SCAN
rs233046	C1orf180	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85809200-85838400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:85814200-85839600	Weak transcription	Left Ventricle	heart
3	chr1:85816000-85831400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:85816000-85839600	Weak transcription	Pancreas	Pancrea
5	chr1:85816600-85836800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:85823200-85836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:85824400-85833800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:85824600-85829600	Enhancers	NHLF	lung
9	chr1:85825000-85839000	Weak transcription	Aorta	Aorta
10	chr1:85825200-85830400	Enhancers	Osteobl	bone
11	chr1:85825400-85829600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:85825600-85829600	Enhancers	Fetal Lung	lung
13	chr1:85826200-85832000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:85826200-85838800	Weak transcription	Hela-S3	cervix
15	chr1:85826400-85831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:85826800-85829600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:85826800-85829800	Enhancers	Fetal Stomach	stomach
18	chr1:85826800-85830000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:85826800-85831000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:85827000-85833800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:85827000-85834600	Enhancers	NHDF-Ad	bronchial
22	chr1:85827000-85837800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:85827200-85831400	Weak transcription	Ovary	ovary
24	chr1:85827200-85831400	Weak transcription	HUVEC	blood vessel
25	chr1:85827200-85832200	Weak transcription	HMEC	breast
26	chr1:85827200-85836800	Weak transcription	Adipose Nuclei	Adipose
27	chr1:85827200-85839000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:85827400-85830000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:85827400-85839400	Weak transcription	Fetal Intestine Large	intestine
30	chr1:85827600-85831200	Weak transcription	Small Intestine	intestine
31	chr1:85827600-85831600	Weak transcription	NH-A	brain
32	chr1:85827600-85836800	Weak transcription	HepG2	liver
33	chr1:85827800-85832000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:85828000-85829600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:85828000-85829600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:85828000-85829600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:85828000-85838800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:85828200-85830200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:85828400-85831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:85828800-85829600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:85828800-85829800	Enhancers	Liver	Liver
42	chr1:85828800-85830000	Enhancers	Psoas Muscle	Psoas
43	chr1:85829000-85829600	Enhancers	HSMMtube	muscle
44	chr1:85829000-85830200	Genic enhancers	HSMM	muscle
45	chr1:85829200-85830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:85829400-85831800	Weak transcription	A549	lung
47	chr1:85829400-85832600	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:85829400-85836800	Weak transcription	Brain Anterior Caudate	brain
49	chr1:85829400-85838400	Weak transcription	Fetal Kidney	kidney

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