Variant report

Variant	rs11039122
Chromosome Location	chr11:47213117-47213118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:47213116-47213166	SAEC	small airway:	n/a
2	chr11:47213116-47213166	SK-N-SH_RA	brain:	n/a
3	chr11:47213075-47213125	NT2-D1	testis:	n/a
4	chr11:47213075-47213125	HNPCEpiC	eye:	n/a
5	chr11:47213116-47213166	RPTEC	kidney:	n/a
6	chr11:47213075-47213125	GM12891	blood:	n/a
7	chr11:47213116-47213166	PANC-1	pancreas:	n/a
8	chr11:47213075-47213125	HRPEpiC	eye:	n/a
9	chr11:47213116-47213166	HRPEpiC	eye:	n/a
10	chr11:47213075-47213125	ovcar-3	ovarian:	n/a
11	chr11:47213116-47213166	Hela-S3	cervix:	n/a
12	chr11:47213116-47213166	NH-A	brain:	n/a
13	chr11:47213075-47213125	H1-hESC	embryonic stem cell:	embryo
14	chr11:47213075-47213125	IMR90	lung:	fetal
15	chr11:47213075-47213125	Hela-S3	cervix:	n/a
16	chr11:47213075-47213125	SK-N-SH_RA	brain:	n/a
17	chr11:47213075-47213125	SK-N-MC	brain:	n/a
18	chr11:47213075-47213125	HepG2	liver:	n/a
19	chr11:47213116-47213166	HepG2	liver:	n/a
20	chr11:47213075-47213125	HPAEpiC	pulmonary alveolar:	n/a
21	chr11:47213075-47213125	AG04449	skin:	fetal
22	chr11:47213116-47213166	PrEC	prostate:	n/a
23	chr11:47213116-47213166	Caco-2	colon:	n/a
24	chr11:47213116-47213166	K562	blood:	n/a
25	chr11:47213116-47213166	NB4	blood:	n/a
26	chr11:47213116-47213166	NT2-D1	testis:	n/a
27	chr11:47213075-47213125	HCT-116	colon:	n/a
28	chr11:47213075-47213125	AG04450	lung:	fetal
29	chr11:47213075-47213125	AG09319	gingival:	n/a
30	chr11:47213075-47213125	LNCaP	prostate:	n/a
31	chr11:47213116-47213166	HIPEpiC	eye:	n/a
32	chr11:47213116-47213166	GM12891	blood:	n/a
33	chr11:47213116-47213166	HRE	kidney:	n/a
34	chr11:47213075-47213125	HRCEpiC	kidney:	n/a
35	chr11:47213116-47213166	HCM	heart:	n/a
36	chr11:47213075-47213125	PFSK-1	brain:	n/a
37	chr11:47213075-47213125	ProgFib	skin:	n/a
38	chr11:47213075-47213125	SK-N-SH	brain:	n/a
39	chr11:47213116-47213166	HEEpiC	esophagus:	n/a
40	chr11:47213075-47213125	AG09309	skin:	n/a
41	chr11:47213116-47213166	HCT-116	colon:	n/a
42	chr11:47213116-47213166	CMK	blood:	n/a
43	chr11:47213075-47213125	K562	blood:	n/a
44	chr11:47213075-47213125	PrEC	prostate:	n/a
45	chr11:47213116-47213166	BJ	skin:	n/a
46	chr11:47213116-47213166	AG04450	lung:	fetal
47	chr11:47213116-47213166	MCF10A-Er-Src	breast:	n/a
48	chr11:47213075-47213125	GM12892	blood:	n/a
49	chr11:47213075-47213125	HRE	kidney:	n/a
50	chr11:47213116-47213166	HPAEpiC	pulmonary alveolar:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr11:47205217..47215436-chr11:47233934..47241095,26	MCF-7	breast:
2	chr11:47205341..47210329-chr11:47212095..47213798,5	MCF-7	breast:
3	chr11:47205689..47216568-chr11:47232414..47239487,27	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243802	CpG island
ENSG00000134574	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11039131	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11570094	1.00[YRI][hapmap]
rs12365578	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12796744	1.00[YRI][hapmap]
rs12803718	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1685404	0.84[CHB][hapmap]
rs17787966	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2291119	1.00[YRI][hapmap]
rs2291443	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291444	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2856650	1.00[YRI][hapmap]
rs3740690	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752848	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs752850	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7946709	1.00[YRI][hapmap]
rs901750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv975171	chr11:47209667-47215620	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11039122	LRP4	cis	Nerve Tibial	GTEx
rs11039122	CTD-2384B9.1	cis	Nerve Tibial	GTEx
rs11039122	C1QTNF4	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47209200-47216000	Weak transcription	Esophagus	oesophagus
2	chr11:47209400-47213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47209600-47213200	Weak transcription	Right Ventricle	heart
4	chr11:47209800-47214000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:47210200-47214800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:47210200-47226000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:47211200-47213800	Weak transcription	K562	blood
8	chr11:47211200-47215400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:47211400-47213200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:47211400-47213600	Weak transcription	HMEC	breast
11	chr11:47211400-47213800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:47211400-47214800	Weak transcription	NHEK	skin
13	chr11:47211400-47215200	Weak transcription	Osteobl	bone
14	chr11:47211400-47215400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:47211400-47215400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:47211400-47215600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:47211600-47213800	Weak transcription	Fetal Intestine Small	intestine
18	chr11:47211600-47213800	Enhancers	Hela-S3	cervix
19	chr11:47211600-47214800	Weak transcription	Fetal Intestine Large	intestine
20	chr11:47211600-47215400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:47211800-47215600	Weak transcription	NH-A	brain
22	chr11:47212200-47215400	Weak transcription	A549	lung
23	chr11:47212400-47213800	Weak transcription	HepG2	liver
24	chr11:47213000-47216800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:47213000-47216800	Enhancers	Placenta	Placenta

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