Variant report

Variant	rs12804382
Chromosome Location	chr11:66458696-66458697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66458582-66459542	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr11:66458531-66459228	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66458063..66461697-chr11:66462045..66464014,3	K562	blood:
2	chr11:66444530..66447369-chr11:66455344..66460090,5	K562	blood:
3	chr11:66457942..66460126-chr11:66460680..66462377,2	MCF-7	breast:
4	chr11:66457271..66460204-chr11:66608971..66610490,2	MCF-7	breast:
5	chr11:66457898..66462042-chr11:66587171..66589768,3	MCF-7	breast:

No data

Variant related genes	Relation type
SPTBN2	TF binding region
ENSG00000173715	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000173653	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12417769	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577111	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12805133	0.96[ASN][1000 genomes]
rs2276138	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34900764	0.90[EUR][1000 genomes]
rs3741363	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474602	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs477557	0.85[ASN][1000 genomes]
rs4930387	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503250	0.80[EUR][1000 genomes]
rs508443	0.87[ASN][1000 genomes]
rs535211	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs556759	0.80[EUR][1000 genomes]
rs577023	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs577335	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs580910	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6591221	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12804382	CCS	cis	multi-tissue	Pritchard
rs12804382	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs12804382	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs12804382	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66446200-66458800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:66446200-66461400	Weak transcription	K562	blood
3	chr11:66446200-66461800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:66446200-66465800	Weak transcription	A549	lung
5	chr11:66446200-66468000	Weak transcription	Lung	lung
6	chr11:66446200-66468600	Weak transcription	Right Ventricle	heart
7	chr11:66446200-66480200	Weak transcription	Fetal Kidney	kidney
8	chr11:66446200-66485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:66446400-66462400	Weak transcription	Fetal Intestine Large	intestine
10	chr11:66446600-66461800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:66446800-66462200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:66450800-66467000	Strong transcription	Fetal Brain Female	brain
13	chr11:66451000-66462200	Strong transcription	Liver	Liver
14	chr11:66451000-66467000	Strong transcription	Brain Germinal Matrix	brain
15	chr11:66451200-66461800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:66451200-66462200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:66451400-66462400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:66451600-66462000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr11:66451800-66462000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:66451800-66462000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:66452200-66461400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:66452200-66485600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:66452400-66461000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr11:66452400-66461800	Strong transcription	Hela-S3	cervix
25	chr11:66452600-66461400	Strong transcription	Fetal Stomach	stomach
26	chr11:66452600-66461600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:66452600-66462000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:66452800-66461600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:66452800-66473800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:66453000-66483400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:66453400-66461800	Strong transcription	Pancreas	Pancrea
32	chr11:66454000-66461800	Weak transcription	Spleen	Spleen
33	chr11:66454000-66462000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:66454000-66462400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:66455000-66462400	Weak transcription	Thymus	Thymus
36	chr11:66455200-66461800	Weak transcription	NHEK	skin
37	chr11:66455200-66462000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:66455600-66460800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr11:66455800-66461600	Weak transcription	HMEC	breast
40	chr11:66455800-66461800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:66455800-66461800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:66455800-66462000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:66455800-66462000	Strong transcription	Brain Anterior Caudate	brain
44	chr11:66456200-66462000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:66456400-66459200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:66456400-66461800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:66456400-66494600	Weak transcription	Right Atrium	heart
48	chr11:66456600-66459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:66456600-66461200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:66456800-66460600	Strong transcription	Brain Cingulate Gyrus	brain

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