Variant report

Variant	rs3741363
Chromosome Location	chr11:66451184-66451185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66445090..66448059-chr11:66449864..66453256,5	K562	blood:
2	chr11:66444892..66446996-chr11:66448996..66453330,4	MCF-7	breast:
3	chr11:66449459..66452348-chr11:66452621..66454965,2	K562	blood:
4	chr11:66450885..66452663-chr11:66600474..66602578,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173898	Chromatin interaction
ENSG00000173914	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12417769	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577111	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804382	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12805133	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1671062	0.86[JPT][hapmap]
rs1671063	0.81[JPT][hapmap]
rs1671064	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs1791684	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1815739	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2276138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513658	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs34900764	0.88[EUR][1000 genomes]
rs474602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs477557	0.86[ASN][1000 genomes]
rs486584	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap]
rs4930387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930391	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs498045	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs503250	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs508443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs509556	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs535211	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540874	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs543191	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs556759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs560556	0.81[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs566673	0.85[CEU][hapmap]
rs569818	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs572846	0.81[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs577023	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs577335	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs580910	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs594313	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs608248	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs618838	0.83[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs627330	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6591221	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs677488	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap]
rs678397	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs692892	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs8432	0.86[JPT][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3741363	PRDX5	cis	cerebellum	SCAN
rs3741363	CTSF	cis	cerebellum	SCAN
rs3741363	UNC93B1	cis	cerebellum	SCAN
rs3741363	CDC42EP2	cis	cerebellum	SCAN
rs3741363	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs3741363	CCS	cis	lymphoblastoid	seeQTL
rs3741363	BBS1	cis	cerebellum	SCAN
rs3741363	YIF1A	cis	cerebellum	SCAN
rs3741363	CTSF	cis	parietal	SCAN
rs3741363	CCS	cis	multi-tissue	Pritchard
rs3741363	ACTN3	cis	Muscle Skeletal	GTEx
rs3741363	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs3741363	ACTN3	cis	lymphoblastoid	seeQTL
rs3741363	CCDC85B	cis	parietal	SCAN
rs3741363	TRMT112	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66445600-66452400	Weak transcription	Spleen	Spleen
2	chr11:66446000-66452200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:66446000-66455800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:66446000-66457400	Weak transcription	Gastric	stomach
5	chr11:66446200-66451200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:66446200-66451200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:66446200-66451400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:66446200-66451400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:66446200-66451400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:66446200-66451400	Weak transcription	Esophagus	oesophagus
11	chr11:66446200-66451600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:66446200-66451800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:66446200-66451800	Weak transcription	NHEK	skin
14	chr11:66446200-66452200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:66446200-66452200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:66446200-66452200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:66446200-66452200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:66446200-66452400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:66446200-66452600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:66446200-66452600	Weak transcription	Fetal Stomach	stomach
21	chr11:66446200-66452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:66446200-66453000	Weak transcription	Brain Anterior Caudate	brain
23	chr11:66446200-66453200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:66446200-66453400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:66446200-66453400	Weak transcription	Pancreas	Pancrea
26	chr11:66446200-66453600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:66446200-66453800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:66446200-66454400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:66446200-66456800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:66446200-66457200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr11:66446200-66457800	Weak transcription	Brain Angular Gyrus	brain
32	chr11:66446200-66458800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:66446200-66461400	Weak transcription	K562	blood
34	chr11:66446200-66461800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:66446200-66465800	Weak transcription	A549	lung
36	chr11:66446200-66468000	Weak transcription	Lung	lung
37	chr11:66446200-66468600	Weak transcription	Right Ventricle	heart
38	chr11:66446200-66480200	Weak transcription	Fetal Kidney	kidney
39	chr11:66446200-66485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:66446400-66453600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:66446400-66457400	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:66446400-66462400	Weak transcription	Fetal Intestine Large	intestine
43	chr11:66446600-66452200	Weak transcription	Placenta	Placenta
44	chr11:66446600-66452200	Weak transcription	HMEC	breast
45	chr11:66446600-66452400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:66446600-66452400	Weak transcription	Hela-S3	cervix
47	chr11:66446600-66453800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:66446600-66461800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:66446800-66451400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:66446800-66452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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