Variant report

Variant	rs2736340
Chromosome Location	chr8:11343973-11343974
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	chr7:118857357..118859002-chr8:11343082..11345568,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11990277	0.87[MEX][hapmap]
rs12677843	0.91[MEX][hapmap]
rs13256690	0.82[ASN][1000 genomes]
rs13277113	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1382568	0.96[ASN][1000 genomes]
rs1478887	0.88[ASN][1000 genomes]
rs1478895	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1478900	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1478901	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1531577	0.81[ASN][1000 genomes]
rs1564267	0.89[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs1600249	0.88[CHB][hapmap];0.86[MEX][hapmap]
rs2061831	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244234	0.83[CHB][hapmap]
rs2250412	0.81[JPT][hapmap]
rs2250788	0.85[ASN][1000 genomes]
rs2251056	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2254546	0.86[ASN][1000 genomes]
rs2254660	0.84[ASN][1000 genomes]
rs2280805	0.83[CHB][hapmap]
rs2409780	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2409781	0.87[CHB][hapmap]
rs2618444	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2618473	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2618478	0.83[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2618479	0.83[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2618480	0.85[ASN][1000 genomes]
rs2618481	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2736332	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2736336	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736337	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2736338	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736343	0.84[ASN][1000 genomes]
rs2736344	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2736345	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2736346	0.82[JPT][hapmap]
rs35393613	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4840565	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4840568	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62489069	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7812879	0.80[ASN][1000 genomes]
rs922483	0.87[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9329246	0.87[MEX][hapmap]
rs9657551	0.87[MEX][hapmap]
rs9693589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9694294	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs998682	0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs998683	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762725	chr8:11322997-11350721	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:4)

Disease	PMID	Source
Systemic lupus erythematosus	21408207	GWAS catalog
Systemic lupus erythematosus and Systemic sclerosis	23740937	GWAS catalog
Kawasaki disease	22446961	GWAS catalog
Rheumatoid arthritis	19503088	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2736340	BLK	cis	lymphoblastoid	seeQTL
rs2736340	CLDN23	cis	multi-tissue	Pritchard
rs2736340	FAM167A	cis	lymphoblastoid	seeQTL
rs2736340	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs2736340	FAM167A	cis	Whole Blood	GTEx
rs2736340	BLK	cis	Lymphoblastoid	GTEx
rs2736340	BLK	cis	multi-tissue	Pritchard
rs2736340	FAM167A	cis	Lymphoblastoid	GTEx
rs2736340	C8orf13	cis	multi-tissue	Pritchard
rs2736340	C8orf13	Cis_1M	lymphoblastoid	RTeQTL
rs2736340	FAM167A	cis	lymphoblastoid	GTEx
rs2736340	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11338200-11350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:11339000-11353800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:11342200-11348600	ZNF genes & repeats	GM12878-XiMat	blood
4	chr8:11343200-11344400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr8:11343400-11344000	Enhancers	Primary B cells from cord blood	blood
6	chr8:11343800-11344200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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