Variant report

Variant	rs541207
Chromosome Location	chr11:64125142-64125143
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:64124546-64127782	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:64125026-64127534	K562	blood:	n/a	n/a
3	SMARCC2	chr11:64124862-64126548	Hela-S3	cervix:	n/a	n/a
4	ZBTB7A	chr11:64125127-64127287	K562	blood:	n/a	n/a
5	MAZ	chr11:64124649-64125918	IMR90	lung:	n/a	chr11:64125278-64125288 chr11:64125274-64125284 chr11:64125725-64125735
6	SMARCC1	chr11:64125052-64126564	Hela-S3	cervix:	n/a	n/a
7	JUN	chr11:64124797-64127116	K562	blood:	n/a	chr11:64125503-64125511
8	POLR2A	chr11:64125002-64125591	GM12892	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63972047..63977847-chr11:64122012..64128099,8	K562	blood:
2	chr11:64082853..64088243-chr11:64119014..64129028,17	MCF-7	breast:
3	chr11:64073021..64075424-chr11:64122972..64125774,2	MCF-7	breast:
4	chr11:64123441..64125427-chr11:64411243..64414199,2	K562	blood:
5	chr11:64083884..64087111-chr11:64122613..64125426,3	K562	blood:
6	chr11:64017685..64020898-chr11:64124130..64127721,3	MCF-7	breast:
7	chr11:64000008..64002901-chr11:64125113..64127418,2	MCF-7	breast:
8	chr11:64109695..64112245-chr11:64123699..64125269,2	MCF-7	breast:
9	chr11:64070986..64076286-chr11:64124810..64128616,7	K562	blood:
10	chr11:64119430..64124364-chr11:64124831..64128743,7	MCF-7	breast:
11	chr11:64004012..64005762-chr11:64124323..64126720,2	MCF-7	breast:
12	chr11:64062668..64065011-chr11:64124225..64126837,3	MCF-7	breast:
13	chr11:64124497..64126994-chr11:64509396..64512374,2	K562	blood:
14	chr11:64124700..64125223-chr11:64215943..64216561,2	MCF-7	breast:
15	chr11:64053151..64055063-chr11:64124109..64127002,2	K562	blood:
16	chr11:64083913..64086967-chr11:64122125..64127376,8	MCF-7	breast:
17	chr11:64080620..64083894-chr11:64124180..64128334,3	MCF-7	breast:
18	chr11:64124989..64126699-chr11:64216058..64218143,2	K562	blood:
19	chr11:64124540..64126165-chr11:64416805..64418709,2	MCF-7	breast:
20	chr11:63972384..63977847-chr11:64121311..64126015,8	K562	blood:
21	chr11:64007008..64012234-chr11:64122125..64125548,6	K562	blood:

No data

Variant related genes	Relation type
RPS6KA4	TF binding region
ENSG00000168071	Chromatin interaction
ENSG00000181908	Chromatin interaction
ENSG00000207024	Chromatin interaction
ENSG00000126432	Chromatin interaction
ENSG00000173511	Chromatin interaction
ENSG00000237410	Chromatin interaction
ENSG00000149781	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000173113	Chromatin interaction
ENSG00000219435	Chromatin interaction
ENSG00000173486	Chromatin interaction
ENSG00000173264	Chromatin interaction
ENSG00000149782	Chromatin interaction
ENSG00000110011	Chromatin interaction
ENSG00000256116	Chromatin interaction
ENSG00000182450	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10897488	0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs11606081	0.89[GIH][hapmap];0.80[TSI][hapmap]
rs1199047	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2282548	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs474901	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4930155	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs508168	0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs510372	0.86[GIH][hapmap];0.87[MEX][hapmap]
rs516124	0.89[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs519763	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs521950	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs527465	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs538147	0.89[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs542907	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs600377	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs612448	0.92[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs615540	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs645078	0.88[GIH][hapmap];0.82[MEX][hapmap]
rs647152	0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
8	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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 miRNA target site	237 gene(s)	inside rSNPs	diseases
9	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
10	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' 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	180 gene(s)	inside rSNPs	diseases
11	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
12	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
13	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
14	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
16	nsv818840	chr11:64097233-64125142	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
17	nsv818841	chr11:64097233-64129722	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
18	nsv897688	chr11:64107735-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
19	nsv897689	chr11:64109118-64148420	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer 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 miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
20	nsv897690	chr11:64118422-64135298	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
21	nsv897691	chr11:64118422-64137875	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
22	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs541207	FKBP2	cis	parietal	SCAN
rs541207	CCDC88B	cis	multi-tissue	Pritchard
rs541207	CCDC88B	cis	cerebellum	SCAN
rs541207	ASRGL1	cis	parietal	SCAN
rs541207	CCDC88B	cis	Cerebellum	GTEx
rs541207	AP003774.1	cis	Whole Blood	GTEx
rs541207	TAF6L	cis	parietal	SCAN
rs541207	MEN1	cis	cerebellum	SCAN
rs541207	PLA2G16	cis	cerebellum	SCAN
rs541207	C11orf68	cis	cerebellum	SCAN
rs541207	FKBP2	cis	cerebellum	SCAN
rs541207	FLJ37970	cis	multi-tissue	Pritchard
rs541207	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64110200-64125200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:64115400-64125600	Weak transcription	GM12878-XiMat	blood
3	chr11:64121800-64126000	Enhancers	Placenta	Placenta
4	chr11:64122000-64126000	Enhancers	Fetal Muscle Trunk	muscle
5	chr11:64122800-64125200	Weak transcription	Primary B cells from cord blood	blood
6	chr11:64123000-64125400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr11:64123000-64125400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:64123000-64125800	Weak transcription	Fetal Brain Male	brain
9	chr11:64123000-64126000	Weak transcription	Psoas Muscle	Psoas
10	chr11:64123200-64125400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:64123200-64125400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:64123200-64125400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:64123200-64125400	Weak transcription	Liver	Liver
14	chr11:64123200-64125400	Weak transcription	Brain Anterior Caudate	brain
15	chr11:64123200-64125400	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:64123200-64125400	Weak transcription	Ovary	ovary
17	chr11:64123200-64125400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:64123200-64125400	Weak transcription	Right Atrium	heart
19	chr11:64123200-64125400	Weak transcription	Right Ventricle	heart
20	chr11:64123200-64125400	Weak transcription	HSMM	muscle
21	chr11:64123200-64125400	Weak transcription	NHDF-Ad	bronchial
22	chr11:64123200-64125600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:64123200-64125600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:64123200-64125600	Weak transcription	Brain Germinal Matrix	brain
25	chr11:64123200-64125600	Weak transcription	Left Ventricle	heart
26	chr11:64123200-64125600	Weak transcription	Thymus	Thymus
27	chr11:64123200-64125600	Weak transcription	HSMMtube	muscle
28	chr11:64123200-64125800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr11:64123200-64125800	Weak transcription	Brain Angular Gyrus	brain
30	chr11:64123200-64126000	Weak transcription	Aorta	Aorta
31	chr11:64123200-64126000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr11:64123200-64126000	Enhancers	HMEC	breast
33	chr11:64123200-64126200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:64123400-64125200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:64123400-64125200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:64123400-64125200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:64123400-64125200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr11:64123400-64125200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:64123400-64125200	Weak transcription	Fetal Heart	heart
40	chr11:64123400-64125200	Enhancers	A549	lung
41	chr11:64123400-64125200	Weak transcription	HUVEC	blood vessel
42	chr11:64123400-64125200	Weak transcription	NH-A	brain
43	chr11:64123400-64125200	Weak transcription	NHLF	lung
44	chr11:64123400-64125200	Weak transcription	Osteobl	bone
45	chr11:64123400-64125400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:64123400-64125400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:64123400-64125400	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:64123400-64125400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:64123400-64125400	Weak transcription	Brain Substantia Nigra	brain
50	chr11:64123400-64125400	Weak transcription	Fetal Lung	lung

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