Variant report

Variant	rs10734249
Chromosome Location	chr11:16775254-16775255
allele	A/G
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:5)
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	POLR2A	chr11:16775202-16775891	K562	blood:	n/a	n/a
2	POLR2A	chr11:16775046-16775614	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:16774991-16775545	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:16766485..16768755-chr11:16775247..16777635,2	MCF-7	breast:
2	chr11:16757813..16760661-chr11:16773208..16775705,2	MCF-7	breast:
3	chr11:16761666..16763335-chr11:16773162..16775562,2	K562	blood:
4	chr11:16760348..16763335-chr11:16772878..16775562,2	K562	blood:
5	chr11:16767679..16771451-chr11:16774137..16777840,3	K562	blood:

No data

Variant related genes	Relation type
C11orf58	TF binding region
ENSG00000110693	Chromatin interaction
ENSG00000110696	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10741708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12794768	0.86[EUR][1000 genomes]
rs12799800	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12799969	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12804277	0.86[EUR][1000 genomes]
rs1501451	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1846936	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1967192	0.89[EUR][1000 genomes]
rs1995343	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2221243	0.85[EUR][1000 genomes]
rs34097789	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34812104	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3802963	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3921675	0.87[EUR][1000 genomes]
rs4756860	0.80[EUR][1000 genomes]
rs4756862	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4757428	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4757431	0.85[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4757432	0.92[EUR][1000 genomes]
rs6486310	0.80[EUR][1000 genomes]
rs6486312	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7110136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7117140	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7125008	0.90[EUR][1000 genomes]
rs7125262	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7128484	0.89[EUR][1000 genomes]
rs7931915	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7939889	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7944906	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10734249	C11orf58	cis	cerebellum	SCAN
rs10734249	SLC6A5	cis	parietal	SCAN
rs10734249	TSG101	cis	cerebellum	SCAN
rs10734249	RASSF10	cis	parietal	SCAN
rs10734249	SAA3P	cis	parietal	SCAN
rs10734249	TPH1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16761400-16783000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:16762200-16780200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:16763000-16780600	Strong transcription	Fetal Thymus	thymus
4	chr11:16763200-16776600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:16763200-16780200	Strong transcription	Osteobl	bone
6	chr11:16763400-16780400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:16763600-16780400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:16764000-16781000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr11:16764200-16778000	Strong transcription	Primary B cells from cord blood	blood
10	chr11:16764400-16777800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr11:16764400-16780000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:16764400-16780400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:16764600-16779600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:16764600-16780200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:16764600-16780400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:16764600-16780400	Strong transcription	A549	lung
17	chr11:16764600-16781600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:16765000-16780200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr11:16765000-16780400	Strong transcription	Dnd41	blood
20	chr11:16765400-16780000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:16765400-16780400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr11:16765600-16777800	Strong transcription	HMEC	breast
23	chr11:16765800-16775800	Strong transcription	Colonic Mucosa	Colon
24	chr11:16765800-16778000	Strong transcription	HUVEC	blood vessel
25	chr11:16765800-16779600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:16765800-16779800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:16765800-16780200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:16765800-16780400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:16765800-16780600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:16765800-16780600	Strong transcription	Placenta	Placenta
31	chr11:16766000-16775800	Strong transcription	HepG2	liver
32	chr11:16766000-16778400	Strong transcription	Ovary	ovary
33	chr11:16766000-16779800	Strong transcription	Hela-S3	cervix
34	chr11:16766000-16780200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:16766000-16780200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:16766000-16780800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:16766000-16781000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:16766200-16776800	Strong transcription	HSMM	muscle
39	chr11:16766200-16778800	Strong transcription	Liver	Liver
40	chr11:16766200-16780200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr11:16766200-16780600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:16766200-16780600	Strong transcription	Fetal Intestine Large	intestine
43	chr11:16766400-16777800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:16766400-16778000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:16766400-16779800	Strong transcription	NH-A	brain
46	chr11:16766400-16780400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:16766600-16777600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:16766600-16778200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:16766600-16780800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:16766800-16776400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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