Variant report

Variant	rs2926228
Chromosome Location	chr8:110367187-110367188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110367154..110368799-chr8:110372886..110376346,3	K562	blood:
2	chr8:110365000..110368622-chr8:110368906..110372128,4	K562	blood:
3	chr8:110367088..110368622-chr8:110370242..110371743,2	K562	blood:
4	chr8:110357510..110359892-chr8:110365729..110367920,2	K562	blood:
5	chr8:110364601..110367292-chr8:110373403..110375892,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205038	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10088918	0.85[CHD][hapmap]
rs10092693	0.85[CHD][hapmap]
rs10098672	0.93[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10099126	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1037695	0.92[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10458302	0.82[CHD][hapmap]
rs12334438	0.82[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs12679728	0.85[CHD][hapmap]
rs12681579	0.87[CHD][hapmap]
rs13252234	0.85[CHD][hapmap]
rs13253951	0.85[CHD][hapmap]
rs13254245	0.85[CHD][hapmap]
rs13278812	0.93[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1379369	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs1379370	0.93[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs1457284	0.89[CEU][hapmap]
rs1457286	0.93[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs1457287	0.92[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1457289	0.93[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs1457290	0.88[CEU][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs1457291	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1458918	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458919	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1471124	0.85[CEU][hapmap]
rs1471125	0.85[CEU][hapmap]
rs1585294	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1626759	0.85[CEU][hapmap];0.82[CHD][hapmap]
rs1627570	0.84[CEU][hapmap]
rs1673390	0.89[CEU][hapmap]
rs1673393	0.89[CEU][hapmap]
rs1673396	0.85[CEU][hapmap]
rs1673398	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs1673400	0.85[CEU][hapmap]
rs1673401	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs1673404	0.85[CEU][hapmap]
rs1673405	0.89[CEU][hapmap]
rs1673407	0.89[CEU][hapmap];0.80[CHD][hapmap];0.82[TSI][hapmap]
rs1673408	0.89[CEU][hapmap];0.80[CHD][hapmap];0.82[TSI][hapmap]
rs1783142	0.85[CEU][hapmap]
rs1783143	0.85[CEU][hapmap]
rs1783144	0.89[CEU][hapmap];0.80[CHD][hapmap];0.82[TSI][hapmap]
rs1783145	0.85[CEU][hapmap]
rs1783149	0.85[CEU][hapmap]
rs1783151	0.85[CEU][hapmap]
rs1783152	0.81[CEU][hapmap];0.80[CHD][hapmap]
rs1783163	0.89[CEU][hapmap]
rs1840908	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs1870107	0.92[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1870109	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061294	0.92[CEU][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2061295	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2168679	0.92[CEU][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs2199120	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2349436	0.85[CHD][hapmap]
rs2349760	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs2349761	0.85[CHD][hapmap]
rs2607637	0.85[CEU][hapmap]
rs2607638	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs2607639	0.85[CEU][hapmap]
rs2844251	0.89[CEU][hapmap]
rs2844252	0.85[CEU][hapmap]
rs2844253	0.85[CEU][hapmap]
rs2926224	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2926225	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2926236	0.83[EUR][1000 genomes]
rs2926238	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980569	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2980575	0.96[ASN][1000 genomes]
rs2980582	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2980583	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4604408	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs4734212	0.85[CHD][hapmap]
rs4735133	0.92[CEU][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6469256	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6469257	0.88[CEU][hapmap];0.84[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6469260	0.92[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs6469261	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs6469262	0.82[JPT][hapmap]
rs6651203	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6982748	0.92[CEU][hapmap];0.84[CHD][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6987198	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6993467	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6993552	0.85[CHD][hapmap]
rs7002606	0.88[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7002926	0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7015262	0.85[CHD][hapmap]
rs7016085	0.85[CHD][hapmap]
rs7016609	0.85[CHD][hapmap]
rs714994	0.82[CHD][hapmap]
rs7818553	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7819151	0.93[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7840592	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs897838	0.93[CEU][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs921959	0.85[CHD][hapmap]
rs921960	0.93[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs9297425	0.85[CHD][hapmap]
rs964307	0.85[CHD][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	nsv891273	chr8:110219735-110475874	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv891279	chr8:110268104-110450092	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv891280	chr8:110346363-110465481	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2926228	PKHD1L1	cis	multi-tissue	Pritchard
rs2926228	PKHD1L1	cis	Thyroid	GTEx
rs2926228	PKHD1L1	cis	Nerve Tibial	GTEx
rs2926228	RP11-419L20.2	cis	Thyroid	GTEx
rs2926228	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2926228	PKHD1L1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110364800-110374800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:110366800-110367600	Enhancers	Fetal Intestine Large	intestine
3	chr8:110366800-110367600	Enhancers	Fetal Intestine Small	intestine
4	chr8:110367000-110367400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:110367000-110367400	Enhancers	K562	blood

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