Variant report

Variant	rs1199046
Chromosome Location	chr11:64118126-64118127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64118115-64119657	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:63972216..63974902-chr11:64117187..64119607,2	K562	blood:
2	chr11:64109106..64114264-chr11:64115033..64120054,6	MCF-7	breast:
3	chr11:64083348..64086402-chr11:64116093..64121800,6	K562	blood:
4	chr11:63972188..63973716-chr11:64116908..64119607,2	K562	blood:

Variant related genes	Relation type
CCDC88B	TF binding region
ENSG00000149781	Chromatin interaction
ENSG00000126432	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000173113	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10792430	1.00[YRI][hapmap]
rs10897487	0.84[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10897488	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11231757	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11231770	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11231771	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11231772	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11542299	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11601651	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11601860	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11606015	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11606081	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199045	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199047	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1662188	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1783521	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17857342	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2510066	0.92[JPT][hapmap]
rs3132740	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs474901	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs475032	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs479552	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs479777	0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs4930155	0.81[CEU][hapmap]
rs499425	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs508168	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs510372	0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs516124	0.92[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs519763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs521950	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs527465	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs538147	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs542907	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs566128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574087	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs574835	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs600377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs612448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61886886	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61886926	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs627425	0.84[AMR][1000 genomes]
rs645078	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs646153	0.85[AMR][1000 genomes]
rs647152	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs663743	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs694739	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72926005	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72926006	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs876064	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
18	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
19	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
20	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
21	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1199046	CCDC88	cis	multi-tissue	Pritchard
rs1199046	CCDC88B	cis	Lymphoblastoid	GTEx
rs1199046	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs1199046	CCDC88B	cis	Cerebellum	GTEx
rs1199046	AP003774.1	cis	Whole Blood	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64110000-64122400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:64110200-64125000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:64110200-64125200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:64110800-64121400	Strong transcription	Primary T cells from cord blood	blood
5	chr11:64110800-64122400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:64110800-64122400	Weak transcription	Lung	lung
7	chr11:64110800-64122800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:64110800-64123400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:64111000-64121200	Weak transcription	Liver	Liver
10	chr11:64111000-64121800	Weak transcription	Right Ventricle	heart
11	chr11:64111000-64122400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:64111000-64122400	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:64111000-64122400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:64111000-64122400	Weak transcription	Right Atrium	heart
15	chr11:64111000-64122600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:64111000-64124200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:64111000-64125000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:64111200-64121800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:64111200-64121800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:64111200-64122400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:64111400-64119000	Strong transcription	Thymus	Thymus
22	chr11:64111400-64122400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:64111400-64122600	Weak transcription	Gastric	stomach
24	chr11:64111800-64118400	Weak transcription	Placenta	Placenta
25	chr11:64111800-64125000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:64112000-64125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:64112200-64120200	Weak transcription	Fetal Intestine Small	intestine
28	chr11:64112200-64120200	Weak transcription	Fetal Stomach	stomach
29	chr11:64113200-64118400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:64113800-64125000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:64115000-64121600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:64115000-64121600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:64115000-64121800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:64115000-64121800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:64115000-64122400	Weak transcription	K562	blood
36	chr11:64115400-64125600	Weak transcription	GM12878-XiMat	blood
37	chr11:64115800-64125000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:64116000-64122000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:64116200-64119800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:64116200-64121800	Weak transcription	A549	lung
41	chr11:64116200-64122400	Weak transcription	Brain Substantia Nigra	brain
42	chr11:64116200-64122400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr11:64116200-64122400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:64116400-64118400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:64116400-64118600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:64116400-64119200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:64116400-64121600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr11:64116400-64122400	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:64116600-64118800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:64116600-64122600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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