Variant report

Variant	rs2199120
Chromosome Location	chr8:110367653-110367654
allele	G/T
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:

Variant related genes	Relation type
ENSG00000205038	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10088918	0.81[JPT][hapmap]
rs10092693	0.81[JPT][hapmap]
rs10098672	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10099126	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1037695	0.90[EUR][1000 genomes]
rs10458302	0.81[JPT][hapmap]
rs12334438	0.84[EUR][1000 genomes]
rs12679728	0.81[JPT][hapmap]
rs13252234	0.81[JPT][hapmap]
rs13253951	0.81[JPT][hapmap]
rs13254245	0.81[JPT][hapmap]
rs13278812	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1379369	0.90[EUR][1000 genomes]
rs1379370	0.91[EUR][1000 genomes]
rs1457287	0.90[EUR][1000 genomes]
rs1457289	0.91[EUR][1000 genomes]
rs1457290	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];0.94[ASN][1000 genomes]
rs1458919	0.96[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs1585294	0.96[CHB][hapmap];0.91[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870107	0.85[EUR][1000 genomes]
rs1870109	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061294	0.90[EUR][1000 genomes]
rs2061295	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2349436	0.81[JPT][hapmap]
rs2349761	0.81[JPT][hapmap]
rs2926224	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2926225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2926228	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]
rs2926236	0.83[EUR][1000 genomes]
rs2926238	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2980569	0.95[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980575	0.94[ASN][1000 genomes]
rs2980582	0.92[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2980583	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4604408	0.89[EUR][1000 genomes]
rs4734212	0.81[JPT][hapmap]
rs4735133	0.88[EUR][1000 genomes]
rs6469256	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6469257	0.91[EUR][1000 genomes]
rs6469260	0.89[EUR][1000 genomes]
rs6651203	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6982748	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6987198	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6993467	0.83[EUR][1000 genomes]
rs6993552	0.81[JPT][hapmap]
rs7002606	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7002926	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7015262	0.81[JPT][hapmap]
rs7016085	0.81[JPT][hapmap]
rs7016609	0.81[JPT][hapmap]
rs7818553	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7819151	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs897838	0.89[EUR][1000 genomes]
rs897839	0.81[JPT][hapmap]
rs921959	0.81[JPT][hapmap]
rs9297425	0.81[JPT][hapmap]
rs964307	0.81[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2199120	PKHD1L1	cis	multi-tissue	Pritchard
rs2199120	PKHD1L1	cis	Nerve Tibial	GTEx
rs2199120	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2199120	PKHD1L1	cis	Thyroid	GTEx
rs2199120	RP11-419L20.2	cis	Thyroid	GTEx

Chromatin state (count:2 , 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	chr8:110367400-110372600	Weak transcription	K562	blood

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