Variant report

Variant	rs414618
Chromosome Location	chr1:86220418-86220419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1047892	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1047893	0.86[JPT][hapmap]
rs1047895	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10493773	0.81[CEU][hapmap]
rs10493774	0.81[CEU][hapmap]
rs10518350	0.86[JPT][hapmap]
rs10782553	0.83[JPT][hapmap]
rs10873710	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs1094359	0.81[ASN][1000 genomes]
rs11161643	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11161645	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs11161649	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11161662	0.87[EUR][1000 genomes]
rs11578464	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs12075929	0.88[CEU][hapmap]
rs12128916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12564080	0.92[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs12566746	0.86[JPT][hapmap]
rs12739713	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs12756013	0.84[EUR][1000 genomes]
rs12758511	0.83[EUR][1000 genomes]
rs1539444	0.86[JPT][hapmap]
rs1764285	0.83[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1764288	0.90[ASN][1000 genomes]
rs1764289	0.92[ASN][1000 genomes]
rs1764291	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1764292	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1764299	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1775988	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1775990	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs184340	0.83[ASN][1000 genomes]
rs2069208	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2274738	0.81[CEU][hapmap]
rs2389970	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2785081	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2995537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs313727	0.84[ASN][1000 genomes]
rs313729	0.84[ASN][1000 genomes]
rs373787	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3753786	0.86[JPT][hapmap]
rs3767162	0.86[ASN][1000 genomes]
rs3767163	0.81[CEU][hapmap]
rs418979	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs419409	0.98[ASN][1000 genomes]
rs424205	0.98[ASN][1000 genomes]
rs434853	0.98[ASN][1000 genomes]
rs447446	0.98[ASN][1000 genomes]
rs450145	0.84[ASN][1000 genomes]
rs4912441	0.95[ASN][1000 genomes]
rs4949915	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs61783617	0.95[ASN][1000 genomes]
rs6576784	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6667094	0.95[ASN][1000 genomes]
rs6672312	0.86[JPT][hapmap]
rs6697535	0.86[JPT][hapmap]
rs6698578	0.87[CEU][hapmap]
rs6699497	0.86[ASN][1000 genomes]
rs709801	0.81[ASN][1000 genomes]
rs7518312	0.83[EUR][1000 genomes]
rs7532758	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs821379	0.86[ASN][1000 genomes]
rs821381	0.84[ASN][1000 genomes]
rs821386	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821389	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs821393	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs821394	0.81[ASN][1000 genomes]
rs821396	0.81[ASN][1000 genomes]
rs821401	0.84[ASN][1000 genomes]
rs843969	0.81[ASN][1000 genomes]
rs9324154	0.83[ASN][1000 genomes]
rs952837	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9700177	0.86[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3344445	chr1:86212214-86221212	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs414618	ZNHIT6	cis	lymphoblastoid	seeQTL
rs414618	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs414618	RPF1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86207800-86221800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:86220200-86222600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:86220400-86220800	ZNF genes & repeats	Fetal Lung	lung
4	chr1:86220400-86222400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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