Variant report

Variant	rs1673398
Chromosome Location	chr8:110476993-110476994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:110466327..110471648-chr8:110473148..110480342,6	K562	blood:
2	chr8:110474378..110477113-chr8:110557939..110560550,2	K562	blood:
3	chr8:110476428..110479434-chr8:110485234..110488569,3	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10088918	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs10092565	0.83[CHB][hapmap]
rs10092693	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs10097258	0.83[CHB][hapmap]
rs10098672	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs10099126	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs10101522	0.83[CHB][hapmap]
rs1026439	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1037695	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap]
rs10458302	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs10955518	0.83[CHB][hapmap]
rs12334438	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs12544835	0.81[CHB][hapmap]
rs12546429	0.83[CHB][hapmap]
rs12679728	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs12681579	0.92[CHD][hapmap]
rs13252234	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs13253951	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs13254245	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs13254461	0.83[CHB][hapmap]
rs13262995	0.83[CHB][hapmap]
rs13266374	0.83[CHB][hapmap]
rs13266838	0.86[CHB][hapmap]
rs13278812	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.81[EUR][1000 genomes]
rs1379363	0.83[CHB][hapmap]
rs1379364	0.86[CHB][hapmap]
rs1379369	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs1379370	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs1457284	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1457286	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs1457287	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap]
rs1457289	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs1457290	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs1457291	0.81[EUR][1000 genomes]
rs1457292	0.83[CHB][hapmap]
rs1458920	0.83[CHB][hapmap]
rs1471124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1471125	1.00[CEU][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs1563579	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1585294	0.85[CEU][hapmap]
rs1624114	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1627570	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673392	0.96[ASN][1000 genomes]
rs1673393	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673394	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1673396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1673397	1.00[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];0.99[ASN][1000 genomes]
rs1673400	1.00[CEU][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs1673401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs1673403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1673405	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673407	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673429	0.81[EUR][1000 genomes]
rs1783142	1.00[CEU][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs1783143	1.00[CEU][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs1783144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783145	1.00[CEU][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs1783149	1.00[CEU][hapmap];1.00[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];0.96[ASN][1000 genomes]
rs1783150	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs1783152	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1783163	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783164	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1783165	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1824193	0.83[CHB][hapmap]
rs1840908	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs1870107	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.81[EUR][1000 genomes]
rs1870108	0.83[CHB][hapmap]
rs1870109	0.81[EUR][1000 genomes]
rs2061294	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs2061295	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs2124982	0.83[CHB][hapmap]
rs2168679	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap]
rs2349436	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs2349760	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs2349761	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs2607637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844232	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2844251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2926228	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs2980569	0.85[CEU][hapmap]
rs4604408	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs4734212	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs4735133	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.81[EUR][1000 genomes]
rs4735134	0.83[CHB][hapmap]
rs6469256	0.81[EUR][1000 genomes]
rs6469257	0.88[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.81[EUR][1000 genomes]
rs6469260	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs6469261	0.90[CHD][hapmap]
rs6469262	0.86[CHB][hapmap]
rs6982748	0.92[CEU][hapmap];0.94[CHD][hapmap]
rs6987198	0.96[CEU][hapmap]
rs6993467	0.87[CHB][hapmap]
rs6993552	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs7002606	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes]
rs7002926	0.83[CHB][hapmap]
rs7015262	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs7016085	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs7016609	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs714994	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs714995	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7819141	0.83[CHB][hapmap]
rs7819151	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs7840592	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs897838	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs897839	0.83[CHB][hapmap]
rs921958	0.83[CHB][hapmap]
rs921959	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs921960	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap]
rs9297425	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs9642806	0.83[CHB][hapmap]
rs964307	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs9656793	0.83[CHB][hapmap]
rs9656882	0.83[CHB][hapmap]
rs965930	0.83[CHB][hapmap]

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	nsv1018510	chr8:110403496-110504029	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv891281	chr8:110450092-110558622	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1673398	PKHD1L1	Cis_1M	lymphoblastoid	RTeQTL
rs1673398	PKHD1L1	cis	lymphoblastoid	seeQTL
rs1673398	PKHD1L1	cis	multi-tissue	Pritchard
rs1673398	RP11-419L20.2	cis	Thyroid	GTEx
rs1673398	PKHD1L1	cis	Thyroid	GTEx
rs1673398	PKHD1L1	cis	Nerve Tibial	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110463200-110492400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:110476800-110478000	Enhancers	HepG2	liver

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