Variant report

Variant	rs2004679
Chromosome Location	chr8:10135193-10135194
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10130155..10132980-chr8:10133293..10136060,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10086995	1.00[ASN][1000 genomes]
rs10098384	1.00[ASN][1000 genomes]
rs10098637	1.00[ASN][1000 genomes]
rs10101698	1.00[ASN][1000 genomes]
rs10102621	0.80[TSI][hapmap]
rs10103875	0.81[EUR][1000 genomes]
rs10111805	1.00[ASN][1000 genomes]
rs10903325	0.83[CEU][hapmap]
rs11249985	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11249990	0.87[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11249991	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs11774051	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777018	0.85[CEU][hapmap]
rs11778030	1.00[ASN][1000 genomes]
rs11782293	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11783091	0.87[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11783281	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13257313	0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs13258691	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13264133	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13269741	0.83[AMR][1000 genomes]
rs13272537	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17151609	1.00[ASN][1000 genomes]
rs17695316	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2004677	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399330	1.00[ASN][1000 genomes]
rs28526848	1.00[ASN][1000 genomes]
rs28602752	1.00[ASN][1000 genomes]
rs28707596	1.00[ASN][1000 genomes]
rs2952221	1.00[JPT][hapmap]
rs2952224	1.00[JPT][hapmap]
rs2952243	1.00[JPT][hapmap]
rs2952244	1.00[JPT][hapmap]
rs2975689	1.00[ASN][1000 genomes]
rs2975704	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2975705	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2975723	1.00[JPT][hapmap]
rs34514972	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34917779	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35287467	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35524676	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4288377	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4541928	1.00[JPT][hapmap]
rs4570161	0.96[CEU][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4840478	0.84[AMR][1000 genomes]
rs4840479	0.83[CEU][hapmap]
rs4841308	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4841315	0.84[AMR][1000 genomes]
rs4841325	1.00[ASN][1000 genomes]
rs4841326	0.82[MEX][hapmap]
rs55836840	1.00[ASN][1000 genomes]
rs55965226	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6601436	0.83[AMR][1000 genomes]
rs6601438	0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs66533014	1.00[ASN][1000 genomes]
rs7000550	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71516564	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs723609	0.83[AMR][1000 genomes]
rs7812334	1.00[ASN][1000 genomes]
rs7817142	0.81[AMR][1000 genomes]
rs7838059	0.83[AMR][1000 genomes]
rs9650648	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9650649	0.96[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1026335	chr8:10037279-10139782	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1028650	chr8:10101815-10178537	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2004679	MFHAS1	cis	cerebellum	SCAN
rs2004679	XKR6	cis	cerebellum	SCAN
rs2004679	PRSS55	cis	cerebellum	SCAN
rs2004679	FLJ10661	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10123000-10138400	Weak transcription	Spleen	Spleen
2	chr8:10123600-10135400	Weak transcription	Fetal Intestine Small	intestine
3	chr8:10125600-10136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:10128200-10137000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr8:10128400-10138200	Weak transcription	Fetal Brain Female	brain
6	chr8:10130400-10144200	Weak transcription	Liver	Liver
7	chr8:10130600-10137600	Weak transcription	Primary T cells from cord blood	blood
8	chr8:10133800-10136800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:10133800-10139000	Weak transcription	Fetal Brain Male	brain
10	chr8:10134200-10136200	Enhancers	Brain Germinal Matrix	brain
11	chr8:10134200-10147600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr8:10135000-10137000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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