Variant report

Variant	rs1671062
Chromosome Location	chr11:66281538-66281539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66280233..66283147-chr11:66288222..66290856,2	K562	blood:
2	chr11:66275530..66280458-chr11:66280685..66284919,6	K562	blood:
3	chr11:66281474..66283176-chr11:66383771..66385422,2	K562	blood:
4	chr11:66276194..66279522-chr11:66281470..66284393,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256349	Chromatin interaction
ENSG00000174483	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000239306	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10736656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791881	0.86[ASW][hapmap]
rs10791882	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12577111	0.86[JPT][hapmap];0.86[MKK][hapmap]
rs1671063	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1671064	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs1671065	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1700184	0.81[EUR][1000 genomes]
rs1700189	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1791684	0.86[JPT][hapmap]
rs1791686	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1791687	0.85[EUR][1000 genomes]
rs1815739	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs2000939	0.86[ASN][1000 genomes]
rs2276138	0.86[JPT][hapmap]
rs2279863	1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2444846	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3018318	0.84[ASN][1000 genomes]
rs3107024	0.81[ASN][1000 genomes]
rs3741363	0.86[JPT][hapmap]
rs486584	0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap]
rs4930387	0.86[JPT][hapmap]
rs503250	0.82[JPT][hapmap]
rs509556	0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs535211	0.82[JPT][hapmap]
rs540874	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs545009	0.85[ASN][1000 genomes]
rs556759	0.82[JPT][hapmap]
rs560556	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs572846	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs577023	0.86[JPT][hapmap]
rs580910	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs615205	0.84[ASN][1000 genomes]
rs618838	0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs630021	0.84[ASN][1000 genomes]
rs677488	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs678397	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs7925093	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7925108	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8432	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	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
6	nsv934228	chr11:66277759-66288927	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1671062	ACTN3	cis	lymphoblastoid	seeQTL
rs1671062	TIGD3	cis	cerebellum	SCAN
rs1671062	SLC22A20	cis	parietal	SCAN
rs1671062	ACTN3	cis	Muscle Skeletal	GTEx
rs1671062	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs1671062	CTD-3074O7.5	cis	Whole Blood	GTEx
rs1671062	CCS	cis	lymphoblastoid	seeQTL
rs1671062	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs1671062	SLC22A6	cis	cerebellum	SCAN
rs1671062	PRDX5	cis	parietal	SCAN
rs1671062	ACY3	cis	cerebellum	SCAN
rs1671062	MALAT1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66278600-66311000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66278800-66281800	Weak transcription	Pancreas	Pancrea
3	chr11:66278800-66282000	Weak transcription	Left Ventricle	heart
4	chr11:66278800-66286400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:66278800-66286600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:66278800-66287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:66278800-66288000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr11:66278800-66288200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:66278800-66288400	Weak transcription	Colonic Mucosa	Colon
10	chr11:66278800-66290400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:66278800-66290600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:66278800-66294000	Weak transcription	Aorta	Aorta
13	chr11:66278800-66309800	Weak transcription	HSMMtube	muscle
14	chr11:66278800-66312800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:66279000-66281600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:66279000-66281600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:66279000-66281600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:66279000-66281600	Weak transcription	NHDF-Ad	bronchial
19	chr11:66279000-66281800	Weak transcription	Fetal Thymus	thymus
20	chr11:66279000-66281800	Weak transcription	Right Ventricle	heart
21	chr11:66279000-66282400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:66279000-66282600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:66279000-66282800	Weak transcription	Fetal Lung	lung
24	chr11:66279000-66286400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:66279000-66286400	Weak transcription	Brain Substantia Nigra	brain
26	chr11:66279000-66286600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:66279000-66286600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr11:66279000-66287000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:66279000-66288200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:66279000-66288200	Weak transcription	Stomach Mucosa	stomach
31	chr11:66279000-66288400	Weak transcription	GM12878-XiMat	blood
32	chr11:66279000-66290200	Weak transcription	HMEC	breast
33	chr11:66279000-66291200	Weak transcription	Psoas Muscle	Psoas
34	chr11:66279000-66303000	Weak transcription	Primary B cells from cord blood	blood
35	chr11:66279000-66306200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:66279000-66309200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr11:66279000-66313000	Weak transcription	Small Intestine	intestine
38	chr11:66279200-66281600	Weak transcription	Adipose Nuclei	Adipose
39	chr11:66279200-66281600	Weak transcription	Liver	Liver
40	chr11:66279200-66281600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:66279200-66281600	Weak transcription	Osteobl	bone
42	chr11:66279200-66281800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:66279200-66281800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:66279200-66282600	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:66279200-66282600	Weak transcription	NH-A	brain
46	chr11:66279200-66286200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:66279200-66286400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:66279200-66286600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:66279200-66286800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:66279200-66286800	Weak transcription	HepG2	liver

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