Variant report

Variant	rs4653662
Chromosome Location	chr1:225921655-225921656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10915864	0.88[ASN][1000 genomes]
rs10915865	0.90[ASN][1000 genomes]
rs10915866	0.96[ASN][1000 genomes]
rs10915868	0.97[ASN][1000 genomes]
rs11589433	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076509	0.95[ASN][1000 genomes]
rs12077115	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[ASN][1000 genomes]
rs12081218	0.95[ASN][1000 genomes]
rs4653429	0.96[ASN][1000 genomes]
rs4653655	0.94[ASN][1000 genomes]
rs4653660	1.00[ASN][1000 genomes]
rs4653663	0.94[EUR][1000 genomes]
rs7521999	0.88[EUR][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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv525391	chr1:225912620-225928538	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653662	ITPKB	cis	lymphoblastoid	seeQTL
rs4653662	HM13	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225912400-225924200	Weak transcription	Spleen	Spleen
2	chr1:225915200-225933600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:225919200-225923000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:225919400-225923000	Weak transcription	Osteobl	bone
5	chr1:225919600-225922800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:225920800-225921800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:225921000-225921800	Enhancers	Liver	Liver
8	chr1:225921000-225922000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:225921000-225922000	Enhancers	Brain Germinal Matrix	brain
10	chr1:225921000-225922400	Enhancers	Hela-S3	cervix
11	chr1:225921200-225921800	Enhancers	Right Atrium	heart
12	chr1:225921400-225922200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:225921400-225922800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:225921400-225922800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:225921400-225923000	Weak transcription	Fetal Stomach	stomach
16	chr1:225921400-225923000	Weak transcription	Psoas Muscle	Psoas
17	chr1:225921400-225923000	Weak transcription	HepG2	liver
18	chr1:225921400-225925600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:225921400-225934400	Weak transcription	Esophagus	oesophagus
20	chr1:225921600-225922800	Weak transcription	Fetal Lung	lung
21	chr1:225921600-225923000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:225921600-225923000	Weak transcription	Fetal Heart	heart
23	chr1:225921600-225923000	Weak transcription	A549	lung

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