Variant report

Variant	rs496914
Chromosome Location	chr11:64487394-64487395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64485321..64487763-chr11:64492091..64495003,2	K562	blood:
2	chr11:64485672..64488139-chr11:64489786..64491520,2	MCF-7	breast:
3	chr11:64126498..64128019-chr11:64487243..64489770,2	K562	blood:
4	chr11:64479124..64481401-chr11:64485906..64488788,2	K562	blood:
5	chr11:64485500..64487701-chr11:64488311..64491830,5	K562	blood:

Variant related genes	Relation type
ENSG00000110076	Chromatin interaction
ENSG00000162302	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10400348	0.85[EUR][1000 genomes]
rs10792444	0.87[EUR][1000 genomes]
rs10897524	0.92[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231853	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs11231859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143937	1.00[CEU][hapmap]
rs1207181	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12223914	0.86[EUR][1000 genomes]
rs12417551	0.88[EUR][1000 genomes]
rs12575704	0.87[EUR][1000 genomes]
rs1633462	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17146121	0.89[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2003293	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073797	0.90[EUR][1000 genomes]
rs2073798	0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2230414	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267918	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284301	1.00[CEU][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2375335	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959652	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3741398	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs3809076	0.89[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs474707	0.81[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs476037	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes]
rs477549	1.00[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs483962	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs487105	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs489192	1.00[CEU][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.84[EUR][1000 genomes]
rs490980	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs494128	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs523200	1.00[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs523752	0.83[EUR][1000 genomes]
rs532747	0.92[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs547066	0.84[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs555974	0.90[EUR][1000 genomes]
rs569602	0.92[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs580374	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58483071	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589691	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs593394	0.93[EUR][1000 genomes]
rs606458	1.00[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs607389	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs620006	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs624975	0.90[CEU][hapmap]
rs625172	0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs630966	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs633923	0.95[EUR][1000 genomes]
rs637332	1.00[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs667237	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs669976	0.90[CEU][hapmap]
rs674297	0.91[EUR][1000 genomes]
rs677298	1.00[CEU][hapmap]
rs680273	1.00[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs683841	0.84[EUR][1000 genomes]
rs684720	0.84[EUR][1000 genomes]
rs686171	0.86[EUR][1000 genomes]
rs693235	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72643567	0.92[EUR][1000 genomes]
rs72643568	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7938455	0.88[EUR][1000 genomes]
rs7939965	0.89[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh 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	33 gene(s)	inside rSNPs	diseases
11	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	79 gene(s)	inside rSNPs	diseases
12	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
14	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
15	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
17	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
18	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer 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
19	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS 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
20	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
21	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs496914	ANKRD13D	cis	parietal	SCAN
rs496914	PYGM	cis	cerebellum	SCAN
rs496914	TMEM138	cis	cerebellum	SCAN
rs496914	LRRN4CL	cis	cerebellum	SCAN
rs496914	TMEM138	cis	parietal	SCAN
rs496914	MALAT1	cis	parietal	SCAN
rs496914	SF1	cis	multi-tissue	Pritchard
rs496914	EHD1	cis	cerebellum	SCAN
rs496914	SF1	cis	lymphoblastoid	seeQTL
rs496914	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs496914	PYGM	cis	parietal	SCAN
rs496914	CABP2	cis	parietal	SCAN
rs496914	POLA2	cis	cerebellum	SCAN
rs496914	B3GNT1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64480400-64489800	Enhancers	Fetal Brain Male	brain
2	chr11:64482600-64489000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:64485000-64487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:64485600-64489000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:64485800-64487400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:64485800-64488200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:64486000-64488400	Weak transcription	Spleen	Spleen
8	chr11:64486400-64488600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:64487000-64490600	Weak transcription	K562	blood
10	chr11:64487200-64487400	Genic enhancers	Brain Germinal Matrix	brain
11	chr11:64487200-64488000	Enhancers	Fetal Brain Female	brain

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