Variant report

Variant	rs9995011
Chromosome Location	chr4:110652734-110652735
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000109534	Chromatin interaction
ENSG00000138794	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000123739	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10004377	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs11728699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938222	0.84[JPT][hapmap]
rs13117504	0.84[CEU][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1541373	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs2301717	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs3181187	0.85[CEU][hapmap];0.91[LWK][hapmap];0.84[YRI][hapmap]
rs4698782	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5030535	0.85[CEU][hapmap];0.83[YRI][hapmap]
rs5030539	0.85[CEU][hapmap]
rs6533451	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs6831917	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs6854876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674868	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7439493	1.00[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674356	0.89[ASW][hapmap];0.85[CEU][hapmap];0.91[LWK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs7694620	0.89[ASW][hapmap];0.85[CEU][hapmap];0.91[LWK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs9992400	0.85[CEU][hapmap];0.87[LWK][hapmap];0.84[YRI][hapmap];0.86[AFR][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	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv4463	chr4:110647731-110693125	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9995011	CASP6	cis	cerebellum	SCAN
rs9995011	CASP6	cis	parietal	SCAN
rs9995011	LARP7	cis	parietal	SCAN
rs9995011	PLA2G12A	cis	Nerve Tibial	GTEx
rs9995011	RRH	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110651600-110662000	Weak transcription	HepG2	liver
2	chr4:110651800-110657000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:110651800-110657800	Weak transcription	Small Intestine	intestine
4	chr4:110651800-110669400	Weak transcription	Spleen	Spleen
5	chr4:110652000-110662400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:110652000-110682800	Weak transcription	Left Ventricle	heart
7	chr4:110652000-110686000	Weak transcription	Ovary	ovary
8	chr4:110652200-110653000	Enhancers	K562	blood
9	chr4:110652200-110656400	Weak transcription	Liver	Liver
10	chr4:110652200-110656800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:110652200-110657600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:110652400-110652800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr4:110652400-110656600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:110652400-110656800	Weak transcription	Pancreas	Pancrea
15	chr4:110652600-110652800	Enhancers	Hela-S3	cervix
16	chr4:110652600-110654800	Weak transcription	Fetal Intestine Large	intestine
17	chr4:110652600-110655000	Weak transcription	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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