Variant report

Variant	rs1151540
Chromosome Location	chr11:66041807-66041808
allele	G/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	chr11:66041614-66042049	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:66041737-66042136	K562	blood:	n/a	n/a
3	POLR2A	chr11:66041699-66042064	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:66041740-66042043	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:66041379-66042171	GM12892	blood:	n/a	n/a
6	POLR2A	chr11:66041604-66041887	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:66041613-66042142	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:66041426-66042160	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66041439..66043181-chr11:66053492..66056458,2	MCF-7	breast:

Variant related genes	Relation type
CNIH2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10791865	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs10896104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1115508	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151537	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1151539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203798	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1717669	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1892939	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508657	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3016319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521109	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs524859	0.87[GIH][hapmap];0.92[MKK][hapmap]
rs528842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555360	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs555853	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs556595	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs708471	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs708472	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs801731	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs801734	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801735	0.84[EUR][1000 genomes]
rs801736	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801737	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801739	0.89[EUR][1000 genomes]
rs801741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326370	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	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
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1151540	C11orf2	cis	parietal	SCAN
rs1151540	SNX32	cis	parietal	SCAN
rs1151540	RP11-867G23.1	cis	Muscle Skeletal	GTEx
rs1151540	RAB1B	cis	cerebellum	SCAN
rs1151540	PACS1	cis	parietal	SCAN
rs1151540	MRGPRF	cis	parietal	SCAN
rs1151540	RAB1B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66037400-66044600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:66037400-66044800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:66037600-66043600	Strong transcription	Osteobl	bone
4	chr11:66037600-66044600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:66037600-66045000	Genic enhancers	Fetal Thymus	thymus
6	chr11:66037800-66044000	Strong transcription	NHEK	skin
7	chr11:66037800-66044200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:66037800-66044600	Strong transcription	Fetal Intestine Small	intestine
9	chr11:66037800-66044800	Strong transcription	Fetal Stomach	stomach
10	chr11:66038000-66042600	Strong transcription	A549	lung
11	chr11:66038000-66042800	Strong transcription	K562	blood
12	chr11:66038000-66043000	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr11:66038000-66043200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:66038000-66043600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:66038000-66044200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:66038000-66044200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:66038000-66044200	Strong transcription	Brain Cingulate Gyrus	brain
18	chr11:66038000-66044200	Strong transcription	Fetal Intestine Large	intestine
19	chr11:66038000-66044200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr11:66038000-66044200	Strong transcription	NHLF	lung
21	chr11:66038000-66044600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:66038000-66044600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:66038000-66044800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:66038200-66042400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:66038200-66042800	Strong transcription	Fetal Lung	lung
26	chr11:66038200-66043600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:66038200-66043800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:66038200-66044200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:66038200-66044200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr11:66038200-66044200	Strong transcription	Colonic Mucosa	Colon
31	chr11:66038200-66044200	Strong transcription	Lung	lung
32	chr11:66038200-66044200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:66038200-66044600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:66038200-66045000	Weak transcription	Right Atrium	heart
35	chr11:66038400-66044000	Strong transcription	Brain Anterior Caudate	brain
36	chr11:66038400-66044400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr11:66038400-66044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:66038400-66045000	Weak transcription	Fetal Heart	heart
39	chr11:66038400-66045000	Strong transcription	Gastric	stomach
40	chr11:66038400-66045200	Weak transcription	Psoas Muscle	Psoas
41	chr11:66038600-66044000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:66038600-66044000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr11:66038600-66044000	Strong transcription	Placenta	Placenta
44	chr11:66038600-66044000	Strong transcription	Dnd41	blood
45	chr11:66038600-66044400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:66038800-66044200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr11:66038800-66044200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr11:66039000-66042600	Strong transcription	Brain Substantia Nigra	brain
49	chr11:66039000-66042800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:66039000-66043600	Strong transcription	HepG2	liver

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