Variant report

Variant	rs11224517
Chromosome Location	chr11:100800400-100800401
allele	A/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	CEBPB	chr11:100800040-100800441	IMR90	lung:	n/a	n/a
2	RUNX3	chr11:100800129-100800466	GM12878	blood:	n/a	n/a
3	NFIC	chr11:100800121-100800645	GM12878	blood:	n/a	n/a
4	ATF2	chr11:100800086-100800559	GM12878	blood:	n/a	n/a
5	EP300	chr11:100800272-100800647	GM12878	blood:	n/a	n/a
6	SMC3	chr11:100800186-100800404	Hela-S3	cervix:	n/a	n/a
7	RUNX3	chr11:100800031-100800510	GM12878	blood:	n/a	n/a
8	BATF	chr11:100800196-100800422	GM12878	blood:	n/a	n/a
9	BHLHE40	chr11:100800310-100800458	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100790778..100793408-chr11:100799342..100801098,2	MCF-7	breast:
2	chr11:100556941..100559649-chr11:100798656..100801476,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238388	TF binding region
ENSG00000165895	Chromatin interaction
ENSG00000248027	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1047624	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11224511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11224518	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11224519	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11224520	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11224525	1.00[AFR][1000 genomes]
rs11224528	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11224529	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12273212	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12276190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12281097	0.87[AFR][1000 genomes]
rs12281543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12283290	0.93[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12285336	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12286700	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12286931	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12287226	0.87[AFR][1000 genomes]
rs12290272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12417750	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17095808	1.00[YRI][hapmap]
rs17095820	1.00[YRI][hapmap]
rs17646129	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17646702	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17647068	0.93[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17647243	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17648451	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17648695	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17654410	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17654633	0.90[EUR][1000 genomes]
rs17659845	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17713573	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17726649	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17726667	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17726715	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17726918	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17727251	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17727449	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17727789	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17727843	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1940220	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1940222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1944435	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2226640	0.91[EUR][1000 genomes]
rs41392445	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs55952345	0.93[EUR][1000 genomes]
rs56199820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60312663	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7924400	0.82[EUR][1000 genomes]
rs7948907	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7949497	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][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	nsv1048356	chr11:100713096-101058995	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv541154	chr11:100713096-101058995	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100772000-100831400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr11:100773800-100809800	Weak transcription	Left Ventricle	heart
3	chr11:100774800-100812800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:100784000-100808800	Weak transcription	Primary B cells from cord blood	blood
5	chr11:100785400-100838400	Weak transcription	Fetal Intestine Small	intestine
6	chr11:100786800-100806800	Weak transcription	Placenta	Placenta
7	chr11:100790000-100803200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:100790200-100812600	Weak transcription	Stomach Mucosa	stomach
9	chr11:100790400-100806600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:100793400-100807000	Weak transcription	Liver	Liver
11	chr11:100794200-100803000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:100794200-100807000	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:100794400-100812800	Weak transcription	Fetal Stomach	stomach
14	chr11:100795600-100807400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr11:100797600-100811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:100798200-100800400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:100798400-100801000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:100798400-100801000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr11:100798400-100801000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:100798600-100800600	Enhancers	Osteobl	bone
21	chr11:100798600-100800800	Weak transcription	Brain Anterior Caudate	brain
22	chr11:100798600-100801000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:100798600-100801000	Enhancers	NHEK	skin
24	chr11:100798600-100807600	Weak transcription	Ovary	ovary
25	chr11:100798600-100811600	Weak transcription	Fetal Lung	lung
26	chr11:100798600-100812800	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:100798600-100826600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:100798600-100828200	Weak transcription	Gastric	stomach
29	chr11:100798800-100807000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:100798800-100811400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:100798800-100832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:100799000-100801000	Enhancers	HMEC	breast
33	chr11:100799000-100801400	Enhancers	NH-A	brain
34	chr11:100799200-100800800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:100799200-100801000	Enhancers	NHDF-Ad	bronchial
36	chr11:100799200-100804600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:100799200-100812800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:100799200-100812800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:100799400-100801000	Enhancers	HSMM	muscle
40	chr11:100799800-100800600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:100800000-100800800	Enhancers	Hela-S3	cervix
42	chr11:100800000-100801000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:100800000-100801000	Enhancers	Fetal Heart	heart
44	chr11:100800000-100801000	Enhancers	HSMMtube	muscle
45	chr11:100800000-100801400	Enhancers	A549	lung
46	chr11:100800200-100800600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:100800200-100800600	Enhancers	NHLF	lung
48	chr11:100800200-100801000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:100800200-100801000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:100800200-100801000	Flanking Active TSS	GM12878-XiMat	blood

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