Variant report

Variant	rs476037
Chromosome Location	chr11:64369540-64369541
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	chr11:64364289..64366155-chr11:64368879..64370972,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10400348	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792444	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897524	0.81[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10897525	0.88[MEX][hapmap]
rs11231853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11231859	0.89[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11231869	0.88[MEX][hapmap]
rs1143937	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs12417551	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575704	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1633462	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs17146121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003293	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073798	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs2230414	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2267918	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]
rs2284301	0.89[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2375335	0.81[EUR][1000 genomes]
rs2959652	0.89[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes]
rs3741398	0.89[CEU][hapmap];0.94[MEX][hapmap]
rs3809076	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs474707	0.89[MEX][hapmap]
rs477549	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes]
rs483962	0.89[CEU][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes]
rs487105	0.89[CEU][hapmap];0.94[MEX][hapmap];0.80[EUR][1000 genomes]
rs489192	0.89[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs496914	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes]
rs523200	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs532747	0.82[GIH][hapmap];1.00[MEX][hapmap]
rs547066	0.92[GIH][hapmap];1.00[MEX][hapmap]
rs569602	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs580374	0.83[EUR][1000 genomes]
rs58483071	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs589691	0.89[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap]
rs593394	0.80[EUR][1000 genomes]
rs606458	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs607389	0.89[CEU][hapmap]
rs625172	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs637332	0.89[CEU][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes]
rs677298	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs680273	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs693235	0.80[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap]
rs72643567	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72643568	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7939965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
9	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
10	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
11	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
12	nsv555197	chr11:64364291-64376307	Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv897696	chr11:64365796-64412877	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs476037	ANKRD13D	cis	parietal	SCAN
rs476037	POLA2	cis	cerebellum	SCAN
rs476037	TMEM138	cis	parietal	SCAN
rs476037	TMEM138	cis	cerebellum	SCAN
rs476037	CABP2	cis	parietal	SCAN
rs476037	EHD1	cis	cerebellum	SCAN
rs476037	LRRN4CL	cis	cerebellum	SCAN
rs476037	PYGM	cis	parietal	SCAN
rs476037	RAB3IL1	cis	parietal	SCAN
rs476037	B3GNT1	cis	cerebellum	SCAN
rs476037	SF1	cis	lymphoblastoid	seeQTL
rs476037	PYGM	cis	cerebellum	SCAN
rs476037	MALAT1	cis	parietal	SCAN
rs476037	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs476037	SF1	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64367400-64370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:64367600-64372200	Weak transcription	Brain Germinal Matrix	brain
3	chr11:64368200-64369600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:64368200-64375200	Weak transcription	Right Atrium	heart
5	chr11:64369000-64369600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:64369000-64372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:64369200-64370200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:64369200-64370400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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