Variant report

Variant	rs1600249
Chromosome Location	chr8:11359638-11359639
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11358894..11362536-chr8:11363129..11366232,3	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11990277	1.00[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs12674768	0.82[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs12677843	0.86[MEX][hapmap]
rs12677903	0.83[AMR][1000 genomes]
rs13277113	0.83[CHB][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap]
rs1478901	0.83[CHB][hapmap]
rs1585729	0.85[ASN][1000 genomes]
rs2252729	0.82[CHB][hapmap]
rs2280805	0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2409781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2618457	0.83[CHB][hapmap]
rs2618471	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2618476	0.94[CHB][hapmap];0.86[MEX][hapmap]
rs2618481	0.83[CHB][hapmap]
rs2736345	0.82[CHB][hapmap]
rs2736346	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2736347	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736350	0.87[ASN][1000 genomes]
rs2736353	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2736354	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2736355	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2898281	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4840568	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs4841546	0.84[AMR][1000 genomes]
rs6993775	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs922483	0.81[CHD][hapmap]
rs998683	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Rheumatoid arthritis	21452313	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1600249	MFHAS1	cis	cerebellum	SCAN
rs1600249	FAM167A	cis	lymphoblastoid	seeQTL
rs1600249	BLK	cis	multi-tissue	Pritchard
rs1600249	C8orf13	Cis_1M	lymphoblastoid	RTeQTL
rs1600249	CTSB	cis	cerebellum	SCAN
rs1600249	TDH	cis	cerebellum	SCAN
rs1600249	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs1600249	BLK	cis	lymphoblastoid	seeQTL
rs1600249	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11352200-11360400	Weak transcription	Spleen	Spleen
2	chr8:11353200-11361000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr8:11353400-11367200	Enhancers	Fetal Thymus	thymus
4	chr8:11356800-11361200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr8:11357400-11380000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr8:11357800-11363400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:11357800-11366600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:11358000-11361400	Enhancers	Thymus	Thymus
9	chr8:11358000-11364200	Genic enhancers	Primary B cells from cord blood	blood
10	chr8:11358800-11360000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:11358800-11360200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr8:11358800-11360400	Flanking Active TSS	Dnd41	blood
13	chr8:11358800-11361800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr8:11359000-11359800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr8:11359000-11360200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr8:11359200-11361600	Weak transcription	NHDF-Ad	bronchial
17	chr8:11359400-11363400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr8:11359400-11364600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:11359600-11360000	Enhancers	Primary T cells from cord blood	blood
20	chr8:11359600-11360600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr8:11359600-11360600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr8:11359600-11360800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr8:11359600-11360800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr8:11359600-11361000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr8:11359600-11361200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:11359600-11364800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr8:11359600-11365400	Weak transcription	NHEK	skin

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