Variant report

Variant	rs647152
Chromosome Location	chr11:64109118-64109119
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr11:64109118-64109141	K562	blood:	n/a	n/a
2	POLR2A	chr11:64108979-64110358	HL-60	blood:	n/a	n/a
3	POLR2A	chr11:64109034-64110295	HL-60	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64001193..64003368-chr11:64108712..64111498,2	MCF-7	breast:
2	chr11:64108003..64110489-chr11:64126101..64127976,2	MCF-7	breast:
3	chr11:64008607..64011562-chr11:64108610..64113296,4	MCF-7	breast:
4	chr11:64078839..64083408-chr11:64108257..64111409,4	MCF-7	breast:
5	chr11:63951267..63954594-chr11:64105049..64110612,5	MCF-7	breast:
6	chr11:64083618..64086276-chr11:64108878..64111761,4	K562	blood:
7	chr11:64072715..64075742-chr11:64108562..64111155,5	MCF-7	breast:
8	chr11:64035871..64037932-chr11:64108620..64111379,2	K562	blood:
9	chr11:63972230..63976425-chr11:64106710..64112651,7	K562	blood:
10	chr11:64036423..64038929-chr11:64108620..64112959,5	K562	blood:
11	chr11:64109106..64114264-chr11:64115033..64120054,6	MCF-7	breast:
12	chr11:64070411..64072227-chr11:64108642..64111595,2	MCF-7	breast:
13	chr11:64068655..64075946-chr11:64105786..64111623,11	K562	blood:
14	chr11:64085064..64087232-chr11:64106469..64111767,5	MCF-7	breast:
15	chr11:64108620..64111741-chr11:64119418..64122798,4	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC88B	TF binding region
ENSG00000173153	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000162302	Chromatin interaction
ENSG00000149781	Chromatin interaction
ENSG00000173511	Chromatin interaction
ENSG00000256116	Chromatin interaction
ENSG00000173113	Chromatin interaction
ENSG00000126432	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000173264	Chromatin interaction
ENSG00000173486	Chromatin interaction
ENSG00000219435	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10897488	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs11231757	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11601860	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11606081	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs1199045	0.80[EUR][1000 genomes]
rs1199046	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1199047	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1783521	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2510066	0.88[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs479552	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs479777	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs4930155	0.83[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs499425	0.88[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs508168	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs510372	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs516124	0.83[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs519763	0.81[GIH][hapmap]
rs538147	0.83[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs541207	0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap]
rs566128	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs574087	0.84[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs574835	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs612448	0.81[GIH][hapmap]
rs615540	0.81[ASN][1000 genomes]
rs61886886	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs627425	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs645078	0.83[GIH][hapmap]
rs646153	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs663743	0.83[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs685870	0.82[YRI][hapmap]
rs694739	0.81[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv555192	chr11:64097233-64111928	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	n/a
18	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
19	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
20	nsv555193	chr11:64107143-64120574	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	22 gene(s)	inside rSNPs	diseases
21	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
22	esv3371829	chr11:64108901-64111749	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	19 gene(s)	inside rSNPs	n/a
23	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs647152	SCGB2A2	cis	cerebellum	SCAN
rs647152	CCS	cis	cerebellum	SCAN
rs647152	CTSW	cis	cerebellum	SCAN
rs647152	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs647152	CCDC88B	cis	lymphoblastoid	seeQTL
rs647152	CCDC88B	cis	multi-tissue	Pritchard
rs647152	PPP1CA	cis	parietal	SCAN
rs647152	FKBP2	cis	cerebellum	SCAN
rs647152	TAF6L	cis	parietal	SCAN
rs647152	C11orf68	cis	cerebellum	SCAN
rs647152	AP003774.1	cis	Whole Blood	GTEx
rs647152	C11orf68	cis	parietal	SCAN
rs647152	FKBP2	cis	parietal	SCAN
rs647152	CYBASC3	cis	cerebellum	SCAN
rs647152	CCDC88B	cis	cerebellum	SCAN
rs647152	MALAT1	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64099800-64109600	Weak transcription	Liver	Liver
2	chr11:64103000-64109600	Weak transcription	Right Atrium	heart
3	chr11:64103400-64109600	Weak transcription	NH-A	brain
4	chr11:64103800-64109400	Weak transcription	NHEK	skin
5	chr11:64106800-64110400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr11:64107200-64109400	Active TSS	Rectal Smooth Muscle	rectum
7	chr11:64107200-64110000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr11:64107400-64109200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr11:64108000-64109400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr11:64108000-64109400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr11:64108000-64109600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr11:64108000-64110400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr11:64108000-64110800	Enhancers	Lung	lung
14	chr11:64108200-64109400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:64108200-64109600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:64108200-64109600	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr11:64108200-64110200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:64108200-64111200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:64108200-64111800	Enhancers	Placenta	Placenta
20	chr11:64108400-64109200	Enhancers	Small Intestine	intestine
21	chr11:64108400-64109400	Enhancers	Gastric	stomach
22	chr11:64108400-64109400	Weak transcription	Right Ventricle	heart
23	chr11:64108400-64109600	Enhancers	Adipose Nuclei	Adipose
24	chr11:64108400-64109800	Flanking Active TSS	GM12878-XiMat	blood
25	chr11:64108400-64110000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr11:64108400-64110400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr11:64108600-64109200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:64108600-64109400	Enhancers	Primary T cells from cord blood	blood
29	chr11:64108600-64109400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:64108600-64109400	Weak transcription	Brain Substantia Nigra	brain
31	chr11:64108600-64109400	Enhancers	Hela-S3	cervix
32	chr11:64108600-64109600	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr11:64108600-64109600	Enhancers	Brain Anterior Caudate	brain
34	chr11:64108600-64109600	Enhancers	Duodenum Mucosa	Duodenum
35	chr11:64108600-64109600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr11:64108600-64109600	Bivalent Enhancer	Fetal Intestine Large	intestine
37	chr11:64108600-64109600	Bivalent Enhancer	Fetal Stomach	stomach
38	chr11:64108600-64109600	Enhancers	Stomach Mucosa	stomach
39	chr11:64108600-64109800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:64108600-64109800	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr11:64108600-64110000	Enhancers	Primary hematopoietic stem cells	blood
42	chr11:64108600-64110200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr11:64108600-64110800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr11:64108600-64110800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:64108600-64111000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:64108800-64109200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr11:64108800-64109200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr11:64108800-64109200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr11:64108800-64109200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:64108800-64109200	Weak transcription	Placenta Amnion	Placenta Amnion

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