Variant report

Variant	rs6902687
Chromosome Location	chr6:28413491-28413492
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1005126	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10807030	0.82[ASN][1000 genomes]
rs10807031	0.82[ASN][1000 genomes]
rs11751928	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11752919	0.81[CEU][hapmap]
rs11755387	0.91[CHB][hapmap]
rs13190937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193272	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13196606	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13199081	1.00[CHB][hapmap]
rs13203055	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13207208	0.81[CEU][hapmap]
rs13209596	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13215804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13217326	0.87[ASN][1000 genomes]
rs16894011	0.90[CHB][hapmap]
rs16894091	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16894106	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17856167	0.91[CHB][hapmap]
rs2108923	0.82[ASN][1000 genomes]
rs2232427	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs28505234	0.86[ASN][1000 genomes]
rs35908902	0.82[ASN][1000 genomes]
rs3799499	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3799500	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs57071502	0.86[ASN][1000 genomes]
rs58020991	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6905380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6917130	0.80[CEU][hapmap]
rs6931359	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6939966	0.81[CEU][hapmap]
rs6940744	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs71559081	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7740429	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7750526	0.84[ASN][1000 genomes]
rs7754960	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7774981	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9468356	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs9468358	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs9468364	0.90[CHB][hapmap]
rs9969098	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419537	chr6:28412323-28414271	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6902687	ZSCAN23	cis	Heart Left Ventricle	GTEx
rs6902687	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs6902687	AL022393.7	cis	Muscle Skeletal	GTEx
rs6902687	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs6902687	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6902687	ZSCAN23	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28411600-28414400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:28411600-28414400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:28411600-28414400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:28411600-28414600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:28411600-28414600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:28411600-28414600	Weak transcription	NHLF	lung
7	chr6:28411600-28414800	Weak transcription	Aorta	Aorta
8	chr6:28411600-28414800	Weak transcription	Pancreas	Pancrea
9	chr6:28411800-28414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:28411800-28414200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:28411800-28414400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:28411800-28414400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:28411800-28414400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:28411800-28414400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:28411800-28414400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:28411800-28414400	Weak transcription	NH-A	brain
17	chr6:28411800-28414400	Weak transcription	Osteobl	bone
18	chr6:28411800-28414600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:28411800-28414600	Weak transcription	Right Ventricle	heart
20	chr6:28411800-28414600	Weak transcription	HSMM	muscle
21	chr6:28411800-28414600	Weak transcription	HSMMtube	muscle
22	chr6:28412000-28414400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:28412000-28414400	Weak transcription	HMEC	breast
24	chr6:28412000-28414600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:28412000-28414600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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