Variant report

Variant	rs524859
Chromosome Location	chr11:66041079-66041080
allele	A/G
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	chr11:66040947-66041368	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:66040787-66041158	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:66041053-66041087	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66038976..66041430-chr11:66054512..66056823,2	MCF-7	breast:

Variant related genes	Relation type
CNIH2	TF binding region
ENSG00000174851	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10791865	0.87[GIH][hapmap]
rs10896104	0.87[GIH][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1151539	0.87[GIH][hapmap];0.92[MKK][hapmap]
rs1151540	0.87[GIH][hapmap];0.92[MKK][hapmap]
rs1892939	0.86[AFR][1000 genomes]
rs3016319	0.92[YRI][hapmap]
rs4073582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474005	0.87[GIH][hapmap];0.91[MKK][hapmap]
rs479018	0.83[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs528842	0.87[GIH][hapmap];0.92[MKK][hapmap]
rs556595	0.85[GIH][hapmap]
rs801732	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801733	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801738	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801742	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9326370	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs524859	CABP2	cis	parietal	SCAN
rs524859	RAB1B	cis	parietal	SCAN
rs524859	SNX32	cis	parietal	SCAN
rs524859	MRGPRF	cis	parietal	SCAN
rs524859	FRMD8	cis	parietal	SCAN
rs524859	SNX32	cis	cerebellum	SCAN
rs524859	SF3B2	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	chr11:66038200-66041800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr11:66038200-66042400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:66038200-66042800	Strong transcription	Fetal Lung	lung
27	chr11:66038200-66043600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:66038200-66043800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:66038200-66044200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:66038200-66044200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr11:66038200-66044200	Strong transcription	Colonic Mucosa	Colon
32	chr11:66038200-66044200	Strong transcription	Lung	lung
33	chr11:66038200-66044200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:66038200-66044600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:66038200-66045000	Weak transcription	Right Atrium	heart
36	chr11:66038400-66041600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:66038400-66041600	Strong transcription	Thymus	Thymus
38	chr11:66038400-66044000	Strong transcription	Brain Anterior Caudate	brain
39	chr11:66038400-66044400	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr11:66038400-66044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:66038400-66045000	Weak transcription	Fetal Heart	heart
42	chr11:66038400-66045000	Strong transcription	Gastric	stomach
43	chr11:66038400-66045200	Weak transcription	Psoas Muscle	Psoas
44	chr11:66038600-66044000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:66038600-66044000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr11:66038600-66044000	Strong transcription	Placenta	Placenta
47	chr11:66038600-66044000	Strong transcription	Dnd41	blood
48	chr11:66038600-66044400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:66038800-66044200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:66038800-66044200	Strong transcription	Monocytes-CD14+_RO01746	blood

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