Variant report

Variant	rs11143691
Chromosome Location	chr9:71387302-71387303
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71386039..71387711-chr9:71393895..71396057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10448338	0.86[CEU][hapmap]
rs10781282	0.81[CEU][hapmap]
rs10869320	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11142867	1.00[ASN][1000 genomes]
rs11143608	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143715	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11143731	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143741	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143761	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11143777	0.80[CEU][hapmap]
rs11143882	0.80[CEU][hapmap]
rs11143951	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11144027	1.00[ASN][1000 genomes]
rs11144136	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11144152	0.80[CEU][hapmap]
rs11144154	0.80[CEU][hapmap]
rs11144178	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11144181	0.80[CEU][hapmap]
rs11144206	0.82[MEX][hapmap]
rs11144215	0.80[CEU][hapmap]
rs11144305	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11144351	0.82[MEX][hapmap]
rs12000088	1.00[ASN][1000 genomes]
rs12339235	0.88[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12376037	0.80[CEU][hapmap]
rs12376991	0.80[CEU][hapmap]
rs12377033	0.80[CEU][hapmap]
rs12379061	0.80[CEU][hapmap]
rs12380573	0.82[MEX][hapmap]
rs12552102	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555728	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412987	1.00[ASN][1000 genomes]
rs1414951	0.80[CEU][hapmap]
rs1414954	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs17058780	0.80[CEU][hapmap]
rs17391456	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs17391582	0.80[CEU][hapmap]
rs17483165	0.80[CEU][hapmap]
rs4623507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552126	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552130	1.00[ASN][1000 genomes]
rs62552131	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865397	0.82[MEX][hapmap]
rs950786	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11143691	FAM108B1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71374000-71388800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:71378000-71388400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:71378400-71394200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:71378800-71393800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:71378800-71393800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr9:71379000-71389000	Weak transcription	K562	blood
7	chr9:71383000-71388800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:71383600-71393800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:71383800-71393600	Weak transcription	Left Ventricle	heart
10	chr9:71384000-71394200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:71385600-71393800	Weak transcription	Small Intestine	intestine
12	chr9:71385800-71393400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:71385800-71393800	Weak transcription	Right Ventricle	heart
14	chr9:71386200-71393600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:71386400-71390200	Enhancers	Fetal Heart	heart
16	chr9:71386400-71392000	Weak transcription	Stomach Mucosa	stomach
17	chr9:71386600-71393200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:71387000-71387400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:71387000-71387400	Enhancers	Aorta	Aorta
20	chr9:71387000-71387600	Enhancers	Placenta	Placenta
21	chr9:71387000-71394200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr9:71387200-71393800	Weak transcription	Fetal Intestine Large	intestine

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