Variant report

Variant	rs683996
Chromosome Location	chr11:63874943-63874944
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	chr11:63871394..63875273-chr11:63876686..63880197,5	K562	blood:
2	chr11:63870131..63872162-chr11:63874556..63877458,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126500	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1011219	0.83[CEU][hapmap]
rs17773078	0.82[CEU][hapmap]
rs2096706	0.81[TSI][hapmap]
rs632603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641811	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs646384	0.83[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs647304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651359	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660070	0.81[CHD][hapmap]
rs7103915	0.84[CEU][hapmap]
rs947939	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking 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	35 gene(s)	inside rSNPs	diseases
4	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
5	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
6	nsv897653	chr11:63761169-63875456	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh 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	13 gene(s)	inside rSNPs	diseases
7	nsv897654	chr11:63772000-63875456	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
10	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
13	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
14	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
15	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
16	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs683996	ANKRD13D	cis	cerebellum	SCAN
rs683996	NAA40	cis	cerebellum	SCAN
rs683996	TMEM216	cis	parietal	SCAN
rs683996	RBM14	cis	cerebellum	SCAN
rs683996	RCE1	cis	cerebellum	SCAN
rs683996	FKBP2	cis	cerebellum	SCAN
rs683996	CCDC88B	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63863800-63875000	Weak transcription	Spleen	Spleen
2	chr11:63863800-63876600	Weak transcription	Fetal Intestine Small	intestine
3	chr11:63866000-63878800	Weak transcription	Esophagus	oesophagus
4	chr11:63866400-63887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:63867000-63882800	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:63867400-63878400	Weak transcription	HepG2	liver
7	chr11:63869600-63878400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:63870000-63879400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr11:63870000-63884400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:63870200-63875200	Weak transcription	Psoas Muscle	Psoas
11	chr11:63871200-63884200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:63871400-63881000	Weak transcription	Gastric	stomach
13	chr11:63871600-63876000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:63872000-63875000	Enhancers	Placenta	Placenta
15	chr11:63872200-63882400	Weak transcription	Fetal Brain Female	brain
16	chr11:63872600-63876800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:63872600-63877000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:63872800-63883600	Weak transcription	Pancreas	Pancrea
19	chr11:63873200-63875400	Enhancers	Brain Germinal Matrix	brain
20	chr11:63873200-63876400	Weak transcription	Right Ventricle	heart
21	chr11:63873400-63876200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:63873400-63886800	Weak transcription	Colonic Mucosa	Colon
23	chr11:63873800-63878600	Weak transcription	Left Ventricle	heart
24	chr11:63873800-63884200	Weak transcription	Brain Anterior Caudate	brain
25	chr11:63874000-63884200	Weak transcription	Brain Angular Gyrus	brain
26	chr11:63874200-63875000	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:63874200-63876600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:63874200-63880000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:63874200-63881200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:63874200-63882800	Weak transcription	Fetal Stomach	stomach
31	chr11:63874200-63883400	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:63874200-63883800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:63874200-63883800	Weak transcription	Brain Substantia Nigra	brain
34	chr11:63874600-63875400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr11:63874600-63877200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr11:63874800-63875200	Enhancers	Primary B cells from peripheral blood	blood

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