Variant report

Variant	rs318860
Chromosome Location	chr8:50833528-50833529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:50832548..50835126-chr8:50839783..50841421,2	K562	blood:

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10086004	0.82[EUR][1000 genomes]
rs10089399	0.82[EUR][1000 genomes]
rs10090657	0.82[EUR][1000 genomes]
rs10092384	0.82[EUR][1000 genomes]
rs10504092	0.85[EUR][1000 genomes]
rs1074385	0.83[EUR][1000 genomes]
rs11785147	0.82[EUR][1000 genomes]
rs12542041	0.82[EUR][1000 genomes]
rs13251355	0.83[EUR][1000 genomes]
rs13267366	0.81[CEU][hapmap]
rs1352112	0.82[EUR][1000 genomes]
rs1352117	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1385311	0.89[CEU][hapmap]
rs1385974	0.82[EUR][1000 genomes]
rs1385975	0.82[EUR][1000 genomes]
rs1385976	0.81[EUR][1000 genomes]
rs1484807	1.00[MEX][hapmap]
rs1486241	0.82[EUR][1000 genomes]
rs1486242	0.82[EUR][1000 genomes]
rs1486243	0.82[EUR][1000 genomes]
rs1486245	0.83[EUR][1000 genomes]
rs1486251	0.82[EUR][1000 genomes]
rs1486252	0.82[EUR][1000 genomes]
rs1486258	0.82[TSI][hapmap]
rs1552372	0.82[EUR][1000 genomes]
rs1580468	0.83[EUR][1000 genomes]
rs167629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs167630	0.89[CEU][hapmap]
rs172758	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs17674389	0.90[CEU][hapmap]
rs17674783	0.85[EUR][1000 genomes]
rs17747294	0.85[EUR][1000 genomes]
rs17747567	0.85[EUR][1000 genomes]
rs17747896	0.85[EUR][1000 genomes]
rs17747929	0.85[EUR][1000 genomes]
rs182646	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2129162	0.83[EUR][1000 genomes]
rs2129165	0.83[EUR][1000 genomes]
rs2170953	0.85[TSI][hapmap]
rs2200494	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs223081	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2385544	0.85[EUR][1000 genomes]
rs2385545	0.82[EUR][1000 genomes]
rs2385546	0.83[EUR][1000 genomes]
rs2385547	0.83[EUR][1000 genomes]
rs2385548	0.83[EUR][1000 genomes]
rs2385554	0.85[TSI][hapmap]
rs2449957	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2449958	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2449959	0.84[EUR][1000 genomes]
rs2450285	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2450288	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2450291	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2628417	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2630550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs318862	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs318864	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs318870	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs318871	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs318872	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318873	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318875	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318877	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs318884	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318888	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318890	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318893	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs318894	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs318902	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs318903	0.89[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs318905	0.89[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs318906	0.89[CEU][hapmap]
rs318908	0.89[CEU][hapmap]
rs318910	0.89[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs318911	0.89[CEU][hapmap]
rs318912	0.89[CEU][hapmap]
rs365318	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs366526	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs380279	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs384406	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs391798	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs402156	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs406337	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs415276	0.90[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs417918	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs436688	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4377975	0.86[EUR][1000 genomes]
rs4383988	0.82[EUR][1000 genomes]
rs4584153	0.82[EUR][1000 genomes]
rs55920504	0.86[EUR][1000 genomes]
rs57585353	0.85[EUR][1000 genomes]
rs58597929	0.86[EUR][1000 genomes]
rs59405147	0.84[EUR][1000 genomes]
rs60061614	0.85[EUR][1000 genomes]
rs6472722	1.00[CEU][hapmap]
rs7008924	0.82[EUR][1000 genomes]
rs7013903	0.82[EUR][1000 genomes]
rs72638307	0.85[EUR][1000 genomes]
rs72638311	0.85[EUR][1000 genomes]
rs72638312	0.85[EUR][1000 genomes]
rs72638332	0.85[EUR][1000 genomes]
rs72638338	0.86[EUR][1000 genomes]
rs7825552	0.82[EUR][1000 genomes]
rs9298228	0.82[EUR][1000 genomes]
rs9298229	0.82[EUR][1000 genomes]
rs964011	0.82[EUR][1000 genomes]
rs967109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs967110	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs967116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9886451	0.82[EUR][1000 genomes]
rs993552	0.89[CEU][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	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs318860	SNTG1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50828200-50833800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:50828600-50836000	Weak transcription	Fetal Brain Female	brain
3	chr8:50828800-50834200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:50830000-50833600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr8:50830200-50834800	Weak transcription	Brain Germinal Matrix	brain
6	chr8:50831800-50834800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:50832000-50841800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:50833000-50838000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr8:50833200-50836000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:50833400-50834800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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