Variant report

Variant	rs5778
Chromosome Location	chr8:110132420-110132421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10081564	0.80[ASN][1000 genomes]
rs10086023	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10088496	0.83[ASN][1000 genomes]
rs10089544	0.83[ASN][1000 genomes]
rs10091155	0.81[ASN][1000 genomes]
rs10098145	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10101048	0.83[ASN][1000 genomes]
rs10101050	0.83[ASN][1000 genomes]
rs10101189	0.83[ASN][1000 genomes]
rs10101520	0.83[ASN][1000 genomes]
rs10505126	0.86[ASN][1000 genomes]
rs10955505	0.86[ASN][1000 genomes]
rs10955508	0.83[ASN][1000 genomes]
rs10955510	0.83[ASN][1000 genomes]
rs10955511	0.81[ASN][1000 genomes]
rs10955512	0.83[ASN][1000 genomes]
rs10955513	0.81[ASN][1000 genomes]
rs11775991	0.83[ASN][1000 genomes]
rs11778370	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11785243	0.83[ASN][1000 genomes]
rs11785269	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985765	0.84[ASN][1000 genomes]
rs11986161	0.83[ASN][1000 genomes]
rs11992816	0.84[ASN][1000 genomes]
rs11994164	0.83[ASN][1000 genomes]
rs11994227	0.83[ASN][1000 genomes]
rs11995419	0.81[ASN][1000 genomes]
rs11997974	0.83[ASN][1000 genomes]
rs12542811	0.83[ASN][1000 genomes]
rs12542959	0.83[ASN][1000 genomes]
rs12543246	0.85[ASN][1000 genomes]
rs12544150	0.83[ASN][1000 genomes]
rs12544462	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12544503	0.83[ASN][1000 genomes]
rs12549347	0.83[ASN][1000 genomes]
rs12549397	0.83[ASN][1000 genomes]
rs12550383	0.83[ASN][1000 genomes]
rs12675753	0.83[ASN][1000 genomes]
rs12679311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12679958	0.80[ASN][1000 genomes]
rs12680028	0.84[ASN][1000 genomes]
rs12680451	0.81[ASN][1000 genomes]
rs12682610	0.81[ASN][1000 genomes]
rs13251321	0.80[ASN][1000 genomes]
rs13251597	0.81[ASN][1000 genomes]
rs13254233	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13265151	0.83[ASN][1000 genomes]
rs13269597	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13282488	0.83[ASN][1000 genomes]
rs1380096	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1380097	0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap]
rs1458915	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1458916	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1458917	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1548082	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs1548083	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs1585295	0.81[ASN][1000 genomes]
rs16892486	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs16892496	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28407429	0.81[ASN][1000 genomes]
rs28413119	0.83[ASN][1000 genomes]
rs28437828	0.83[ASN][1000 genomes]
rs2926198	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2980603	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2980618	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2980624	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs34049275	0.81[ASN][1000 genomes]
rs34092076	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35850605	0.81[ASN][1000 genomes]
rs35978837	0.83[ASN][1000 genomes]
rs3890699	0.81[ASN][1000 genomes]
rs3925087	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3925088	0.83[ASN][1000 genomes]
rs4129682	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4130640	0.81[ASN][1000 genomes]
rs4130682	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4236801	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4236802	0.86[ASN][1000 genomes]
rs4236803	0.81[ASN][1000 genomes]
rs4236804	0.81[ASN][1000 genomes]
rs4257986	0.81[ASN][1000 genomes]
rs4265160	0.81[ASN][1000 genomes]
rs4288351	0.81[ASN][1000 genomes]
rs4301422	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4311632	0.81[ASN][1000 genomes]
rs4332104	0.81[ASN][1000 genomes]
rs4339614	0.81[ASN][1000 genomes]
rs4342559	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4358779	0.83[ASN][1000 genomes]
rs4386952	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4389899	0.83[ASN][1000 genomes]
rs4389900	0.81[ASN][1000 genomes]
rs4428648	0.83[ASN][1000 genomes]
rs4439099	0.83[ASN][1000 genomes]
rs4442117	0.83[ASN][1000 genomes]
rs4443632	0.83[ASN][1000 genomes]
rs4446710	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454252	0.81[ASN][1000 genomes]
rs4464939	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4529440	0.83[ASN][1000 genomes]
rs4546626	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570131	0.81[ASN][1000 genomes]
rs4645539	0.83[ASN][1000 genomes]
rs4734190	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734191	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4734196	0.83[ASN][1000 genomes]
rs4734197	0.83[ASN][1000 genomes]
rs4734198	0.83[ASN][1000 genomes]
rs4734203	0.81[ASN][1000 genomes]
rs4734204	0.81[ASN][1000 genomes]
rs4735091	0.84[ASN][1000 genomes]
rs4735092	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4735093	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs4735094	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4735095	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4735096	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4735097	0.89[ASN][1000 genomes]
rs4735098	0.89[ASN][1000 genomes]
rs4735108	0.83[ASN][1000 genomes]
rs4735109	0.83[ASN][1000 genomes]
rs4735110	0.83[ASN][1000 genomes]
rs4735114	0.81[ASN][1000 genomes]
rs56896876	0.83[ASN][1000 genomes]
rs62511091	0.81[ASN][1000 genomes]
rs6983376	0.83[ASN][1000 genomes]
rs6985869	0.81[ASN][1000 genomes]
rs6986127	0.80[ASN][1000 genomes]
rs6990140	0.83[ASN][1000 genomes]
rs6994788	0.80[ASN][1000 genomes]
rs6998731	0.81[ASN][1000 genomes]
rs6998883	0.81[ASN][1000 genomes]
rs7010380	0.83[ASN][1000 genomes]
rs720574	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs7817746	0.81[ASN][1000 genomes]
rs7817909	0.81[ASN][1000 genomes]
rs7821463	0.84[ASN][1000 genomes]
rs7823804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825689	0.83[ASN][1000 genomes]
rs7828207	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829544	0.89[ASN][1000 genomes]
rs7832552	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7840000	0.84[ASN][1000 genomes]
rs7844643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845815	0.83[ASN][1000 genomes]
rs9297421	0.89[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	nsv1022273	chr8:110026712-110146600	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv539715	chr8:110026712-110146600	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5778	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs5778	PKHD1L1	cis	lymphoblastoid	seeQTL
rs5778	NUDCD1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110121400-110144600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:110130400-110133600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr8:110131000-110133600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr8:110131000-110133800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr8:110131200-110132800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:110131200-110133400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr8:110131400-110133400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr8:110131600-110133600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr8:110131600-110133800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:110131800-110132800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:110131800-110132800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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