Variant report

Variant	rs10491353
Chromosome Location	chr5:58575133-58575134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10054481	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10472101	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10472102	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11955452	0.81[JPT][hapmap]
rs12655617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12658554	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374028	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs28372523	0.88[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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10491353	PART1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58571800-58579400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58572000-58582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:58572200-58583000	Weak transcription	Left Ventricle	heart
4	chr5:58572400-58575800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:58572800-58575200	Weak transcription	Fetal Intestine Large	intestine
6	chr5:58572800-58577800	Enhancers	Hela-S3	cervix
7	chr5:58573200-58576000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:58573400-58583400	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:58573600-58576400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:58573600-58582800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:58573600-58583000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:58573600-58583000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:58573800-58576600	Weak transcription	Fetal Heart	heart
14	chr5:58573800-58581400	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:58574000-58575600	Enhancers	A549	lung
16	chr5:58574200-58590200	Weak transcription	Right Atrium	heart
17	chr5:58574800-58582800	Weak transcription	Psoas Muscle	Psoas
18	chr5:58575000-58575400	Enhancers	HUVEC	blood vessel

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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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