Variant report

Variant	rs3775718
Chromosome Location	chr4:143348680-143348681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11728236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144939	1.00[ASW][hapmap];0.81[MKK][hapmap]
rs1489578	1.00[ASW][hapmap]
rs1497389	1.00[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1497398	1.00[YRI][hapmap]
rs17715707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982966	1.00[ASW][hapmap]
rs3775705	1.00[YRI][hapmap]
rs3775710	0.93[AFR][1000 genomes]
rs3775712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3775717	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724573	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724579	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72724580	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7699598	1.00[YRI][hapmap]

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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3775718	LSM6	cis	cerebellum	SCAN
rs3775718	C4orf49	cis	cerebellum	SCAN
rs3775718	GYPB	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143329000-143350000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143338600-143348800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:143338600-143366600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:143339000-143355400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:143345200-143351000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:143346000-143351800	Weak transcription	A549	lung
7	chr4:143346400-143353800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:143346600-143350000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:143347600-143348800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:143347600-143350000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:143347800-143348800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:143347800-143349000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:143348200-143350000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:143348600-143349000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:143348600-143349000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:143348600-143349000	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr4:143348600-143349000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr4:143348600-143349200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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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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