Variant report

Variant	rs6933930
Chromosome Location	chr6:38812471-38812472
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10484847	1.00[CHB][hapmap]
rs11751371	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11756771	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11758334	1.00[CHB][hapmap]
rs12192604	1.00[ASN][1000 genomes]
rs12192779	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12192848	1.00[ASN][1000 genomes]
rs12193813	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12194119	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197467	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206059	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12209734	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215108	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12664132	1.00[CHB][hapmap]
rs13192864	1.00[CHB][hapmap]
rs13201998	1.00[CHB][hapmap]
rs13207718	1.00[CHB][hapmap]
rs1738248	1.00[CHB][hapmap]
rs17421805	1.00[CHB][hapmap]
rs17422753	1.00[CHB][hapmap]
rs17552381	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17552881	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17623162	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17632688	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs1929899	1.00[CHD][hapmap]
rs2092550	1.00[ASN][1000 genomes]
rs4279429	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs45578845	1.00[ASN][1000 genomes]
rs55902132	1.00[ASN][1000 genomes]
rs55933840	1.00[ASN][1000 genomes]
rs56093987	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56148146	1.00[ASN][1000 genomes]
rs56246807	1.00[ASN][1000 genomes]
rs56266437	1.00[ASN][1000 genomes]
rs56284095	1.00[ASN][1000 genomes]
rs56323406	1.00[ASN][1000 genomes]
rs579786	1.00[CHB][hapmap]
rs62396392	1.00[ASN][1000 genomes]
rs62396394	1.00[ASN][1000 genomes]
rs62396399	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62396403	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62396404	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62396406	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62396408	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905213	1.00[CHB][hapmap]
rs6930771	1.00[CHB][hapmap]
rs72856585	1.00[ASN][1000 genomes]
rs72856596	1.00[ASN][1000 genomes]
rs72856597	1.00[ASN][1000 genomes]
rs72856598	1.00[ASN][1000 genomes]
rs72858234	1.00[ASN][1000 genomes]
rs72858240	1.00[ASN][1000 genomes]
rs72858280	1.00[ASN][1000 genomes]
rs72858282	1.00[ASN][1000 genomes]
rs72858286	1.00[ASN][1000 genomes]
rs72858288	1.00[ASN][1000 genomes]
rs72858292	1.00[ASN][1000 genomes]
rs72858299	1.00[ASN][1000 genomes]
rs7760621	0.81[AMR][1000 genomes]
rs7773144	1.00[ASN][1000 genomes]
rs862433	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs991766	1.00[CHB][hapmap];1.00[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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6933930	CLPS	cis	cerebellum	SCAN
rs6933930	PTCRA	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38766800-38824400	Weak transcription	K562	blood
2	chr6:38804600-38821000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:38811600-38812600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:38812000-38814000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:38812400-38812600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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