Variant report

Variant	rs1673408
Chromosome Location	chr8:110455321-110455322
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10088918	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs10092565	0.83[CHB][hapmap]
rs10092693	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs10097258	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs10098672	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10099126	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10101522	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs1026439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1037695	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10458302	0.83[CHB][hapmap];0.92[CHD][hapmap];0.88[ASN][1000 genomes]
rs10955518	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs12334438	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12544835	0.81[CHB][hapmap]
rs12546429	0.83[CHB][hapmap]
rs12550601	0.85[ASN][1000 genomes]
rs12679728	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs12680439	0.84[ASN][1000 genomes]
rs12681579	0.92[CHD][hapmap]
rs13252234	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs13253951	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs13254245	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs13254461	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs13258279	0.88[ASN][1000 genomes]
rs13262995	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs13264576	0.88[ASN][1000 genomes]
rs13264587	0.88[ASN][1000 genomes]
rs13266285	0.84[ASN][1000 genomes]
rs13266293	0.88[ASN][1000 genomes]
rs13266374	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs13266838	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs13267428	0.84[ASN][1000 genomes]
rs13268429	0.84[ASN][1000 genomes]
rs13278812	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1379363	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs1379364	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1379365	0.85[ASN][1000 genomes]
rs1379369	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1379370	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1457286	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs1457287	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457289	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457290	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457291	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1457292	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs1457293	0.85[ASN][1000 genomes]
rs1458920	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs1471124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1471125	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1563579	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1585294	0.89[CEU][hapmap]
rs1624114	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1626759	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1627570	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1673390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1673392	0.86[ASN][1000 genomes]
rs1673393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1673394	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673396	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1673397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1673398	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]
rs1673400	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673401	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673403	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673404	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673405	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673429	0.80[EUR][1000 genomes]
rs16879470	0.84[ASN][1000 genomes]
rs1783142	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1783143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1783144	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783145	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783149	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783150	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1783152	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1783163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783164	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783165	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1824193	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs1840908	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1870107	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1870108	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs1870109	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061294	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2061295	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2124982	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs2168679	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs2349436	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2349760	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2349761	0.83[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs2607637	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2607638	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2607639	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844232	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2844251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844252	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926228	0.89[CEU][hapmap];0.80[CHD][hapmap];0.82[TSI][hapmap]
rs2980569	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs2980582	0.81[CEU][hapmap]
rs4348463	0.85[ASN][1000 genomes]
rs4604408	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734212	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs4735133	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4735134	0.83[CHB][hapmap];0.88[ASN][1000 genomes]
rs6469256	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6469257	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6469260	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6469261	0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6469262	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6982748	0.96[CEU][hapmap];0.94[CHD][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6987198	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6993467	0.87[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6993552	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs6999505	0.83[ASN][1000 genomes]
rs7002606	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7002926	0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7014589	0.88[ASN][1000 genomes]
rs7015262	0.83[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs7016085	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs7016609	0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs714994	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs714995	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7818553	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7819141	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs7819151	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7840592	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs897838	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs897839	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs921958	0.83[CHB][hapmap]
rs921959	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs921960	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs9297425	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs9642806	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs964307	0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs9656793	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs9656882	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs965930	0.83[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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
rs1673408	RP11-419L20.2	cis	Thyroid	GTEx
rs1673408	PKHD1L1	cis	Thyroid	GTEx
rs1673408	PKHD1L1	cis	multi-tissue	Pritchard
rs1673408	PKHD1L1	cis	Nerve Tibial	GTEx
rs1673408	PKHD1L1	cis	lymphoblastoid	seeQTL
rs1673408	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110454200-110455400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:110455000-110455400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr8:110455000-110456400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr8:110455200-110455600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr8:110455200-110455600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:110455200-110455600	Enhancers	K562	blood
7	chr8:110455200-110456000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:110455200-110456000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:110455200-110456200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr8:110455200-110456800	Enhancers	HUES48 Cell Line	embryonic stem cell

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