Variant report

Variant	rs1951627
Chromosome Location	chr1:173891817-173891818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173826105..173828318-chr1:173891336..173894864,3	K562	blood:
2	chr1:173837252..173839626-chr1:173890337..173892494,2	K562	blood:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10798301	0.87[CHB][hapmap]
rs10798302	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10912719	0.82[ASN][1000 genomes]
rs12066153	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12079062	0.83[CHB][hapmap]
rs12097809	0.93[AMR][1000 genomes]
rs12563301	0.87[CHB][hapmap]
rs1322775	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs1322777	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs1322780	0.87[CHB][hapmap];0.90[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs13375086	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16846683	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1799876	0.91[CHB][hapmap];0.85[GIH][hapmap];0.89[YRI][hapmap]
rs1884994	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650945	0.83[CHB][hapmap]
rs4652169	0.87[CHB][hapmap]
rs4971204	0.87[YRI][hapmap]
rs56247945	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56753505	0.86[ASN][1000 genomes]
rs5877	0.90[GIH][hapmap]
rs5878	0.87[CHB][hapmap];0.88[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs6663875	0.87[CHB][hapmap];0.90[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs6665484	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6677660	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs6686083	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6689285	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs6695327	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs6696163	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6699146	0.87[CHB][hapmap]
rs714624	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7413166	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7514069	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7533430	0.83[CHB][hapmap]
rs7547280	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7553788	0.86[CHB][hapmap]
rs9286895	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs941989	0.87[CHB][hapmap];0.90[GIH][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs9425430	0.87[CHB][hapmap];0.90[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs9425766	0.87[CHB][hapmap];0.87[GIH][hapmap];0.83[MKK][hapmap]
rs9425775	0.87[MEX][hapmap]
rs9661233	0.87[CHB][hapmap];1.00[YRI][hapmap]

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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1951627	PRDX6	cis	parietal	SCAN
rs1951627	FMO1	cis	cerebellum	SCAN
rs1951627		cis	Lymphoblastoid	GTEx
rs1951627	CENPL	cis	lymphoblastoid	seeQTL
rs1951627	SNORD78	cis	parietal	SCAN
rs1951627	SERPINC1	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
3	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
4	chr1:173870000-173898000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
6	chr1:173872400-173896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:173879200-173899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:173888400-173900200	Weak transcription	Right Atrium	heart
11	chr1:173888600-173892400	Weak transcription	Liver	Liver
12	chr1:173891200-173899400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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