Variant report

Variant	rs11097200
Chromosome Location	chr4:89761563-89761564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10001319	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022272	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11735482	0.89[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12649368	0.95[MEX][hapmap];0.80[TSI][hapmap]
rs1379934	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1563688	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100679	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34321014	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62308743	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7680357	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11097200	HERC6	cis	parietal	SCAN
rs11097200	GPRIN3	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89745000-89764200	Weak transcription	Ovary	ovary
2	chr4:89745000-89764800	Weak transcription	Pancreas	Pancrea
3	chr4:89745000-89770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:89745000-89775000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:89745200-89776200	Weak transcription	Aorta	Aorta
6	chr4:89749000-89769600	Weak transcription	K562	blood
7	chr4:89752000-89763600	Weak transcription	Small Intestine	intestine
8	chr4:89752000-89764000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:89752000-89778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:89752800-89769200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:89754400-89763200	Weak transcription	Fetal Lung	lung
12	chr4:89754600-89779600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:89755400-89763600	Weak transcription	Fetal Intestine Small	intestine
14	chr4:89756400-89763400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:89756400-89767400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:89756600-89764800	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:89757200-89764400	Weak transcription	Placenta	Placenta
18	chr4:89761200-89761600	Enhancers	HepG2	liver
19	chr4:89761200-89761800	Enhancers	Fetal Intestine Large	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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