Variant report

Variant	rs11677573
Chromosome Location	chr2:172771000-172771001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172747709..172751277-chr2:172768441..172772917,4	K562	blood:
2	chr2:172769606..172772915-chr2:172967149..172970199,3	K562	blood:
3	chr2:172764440..172768356-chr2:172769175..172774540,8	K562	blood:
4	chr2:172763759..172768235-chr2:172769175..172774540,7	K562	blood:
5	chr2:172770788..172773001-chr2:172780545..172783443,2	K562	blood:
6	chr2:172769627..172771187-chr2:172785586..172788506,2	K562	blood:
7	chr2:172769627..172772363-chr2:172785996..172788506,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10177679	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10179020	0.82[AMR][1000 genomes]
rs10185633	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10188587	0.84[ASN][1000 genomes]
rs10191399	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10196521	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1022358	1.00[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10432474	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10439296	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10930498	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10930500	0.84[ASN][1000 genomes]
rs10930501	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1105264	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11676484	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11683436	0.87[ASN][1000 genomes]
rs11692418	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11695887	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11883977	0.82[ASN][1000 genomes]
rs11887208	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11903123	0.82[AMR][1000 genomes]
rs11903410	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12467010	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12468218	0.84[ASN][1000 genomes]
rs12473516	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs12478215	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12479374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12617265	1.00[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12619137	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12692979	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs13017988	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[AFR][1000 genomes]
rs13031370	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13399316	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1400816	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs1443699	0.90[ASN][1000 genomes]
rs1443700	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1543168	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1607253	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1878583	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1982288	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1996425	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2028670	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2028671	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2028672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2028673	0.83[ASN][1000 genomes]
rs2028674	0.83[ASN][1000 genomes]
rs2056202	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2176466	1.00[JPT][hapmap]
rs2292813	0.88[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes]
rs2292814	0.89[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2357064	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2357206	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2357207	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2357208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28372952	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs312917	0.89[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs3770443	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3770444	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3770453	0.84[ASW][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3770457	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs3791343	0.96[ASN][1000 genomes]
rs3821092	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3821094	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes]
rs3821096	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs4072279	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4324292	0.88[JPT][hapmap]
rs4507064	0.81[AMR][1000 genomes]
rs4668417	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4668419	0.83[AFR][1000 genomes]
rs59853867	0.84[ASN][1000 genomes]
rs60706248	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62182438	0.85[ASN][1000 genomes]
rs6433313	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes]
rs6433315	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6433316	0.87[AMR][1000 genomes]
rs6433317	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[AFR][1000 genomes]
rs6433318	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6433322	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6707142	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6708365	0.81[AFR][1000 genomes]
rs6711813	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6714214	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6726050	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6726991	0.80[AFR][1000 genomes]
rs6733123	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6736159	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs6740705	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6742905	1.00[ASN][1000 genomes]
rs6753551	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6753859	0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6757680	1.00[ASW][hapmap];0.88[JPT][hapmap]
rs6758494	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6760680	1.00[JPT][hapmap]
rs7340516	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7371503	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7371631	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7579509	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7580132	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7580232	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7583860	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7588025	0.94[ASW][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs7594478	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7597525	1.00[ASN][1000 genomes]
rs7598232	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs925881	1.00[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs9287948	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs949548	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs970948	0.94[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv536037	chr2:172745597-172780616	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11677573	LASS6	cis	parietal	SCAN
rs11677573	DYNC1I2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172770400-172771000	Enhancers	K562	blood

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