Variant report

Variant	rs12290170
Chromosome Location	chr11:100555218-100555219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr11:100555027-100555407	HepG2	liver:	n/a	n/a
2	TBL1XR1	chr11:100554797-100555257	GM12878	blood:	n/a	n/a
3	FOXA1	chr11:100555033-100555365	HepG2	liver:	n/a	n/a
4	IRF4	chr11:100554781-100555229	GM12878	blood:	n/a	n/a
5	EP300	chr11:100554818-100555603	A549	lung:	n/a	chr11:100554825-100554839
6	FOSL1	chr11:100555098-100556077	HCT-116	colon:	n/a	n/a
7	FOXA1	chr11:100555075-100555478	T-47D	breast:	n/a	n/a
8	REST	chr11:100554917-100555398	A549	lung:	n/a	n/a
9	CUX1	chr11:100554947-100555239	GM12878	blood:	n/a	n/a
10	FOXA2	chr11:100555096-100555343	HepG2	liver:	n/a	n/a
11	EP300	chr11:100554844-100555508	GM12878	blood:	n/a	n/a
12	MEF2C	chr11:100554711-100555279	GM12878	blood:	n/a	n/a
13	FOXA2	chr11:100555042-100555505	A549	lung:	n/a	n/a
14	CHD2	chr11:100554834-100555345	GM12878	blood:	n/a	n/a
15	RUNX3	chr11:100554835-100555251	GM12878	blood:	n/a	n/a
16	EBF1	chr11:100554743-100555343	GM12878	blood:	n/a	n/a
17	FOXA1	chr11:100555098-100555404	T-47D	breast:	n/a	n/a
18	EP300	chr11:100554819-100555514	A549	lung:	n/a	chr11:100554825-100554839
19	RFX5	chr11:100555173-100555501	HepG2	liver:	n/a	n/a
20	TCF12	chr11:100554720-100555672	A549	lung:	n/a	n/a
21	SP1	chr11:100554991-100556200	HCT-116	colon:	n/a	n/a
22	GATA3	chr11:100554997-100555446	A549	lung:	n/a	n/a
23	SP1	chr11:100554923-100555553	A549	lung:	n/a	n/a
24	FOXA2	chr11:100555063-100555439	A549	lung:	n/a	n/a
25	GATA3	chr11:100554826-100555499	A549	lung:	n/a	n/a
26	SP1	chr11:100554853-100555602	A549	lung:	n/a	n/a
27	BHLHE40	chr11:100554850-100555265	GM12878	blood:	n/a	n/a
28	FOXA1	chr11:100555084-100555383	HepG2	liver:	n/a	n/a
29	FOXA1	chr11:100555090-100555415	HepG2	liver:	n/a	n/a
30	RUNX3	chr11:100554754-100555323	GM12878	blood:	n/a	n/a
31	FOSL2	chr11:100554834-100555361	A549	lung:	n/a	n/a
32	EP300	chr11:100554794-100555687	GM12878	blood:	n/a	chr11:100554825-100554839

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:100550243..100553633-chr11:100554741..100557125,4	K562	blood:

No data

Variant related genes	Relation type
ARHGAP42	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11224373	0.80[AMR][1000 genomes]
rs11224388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11224392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12272835	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12282414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv556122	chr11:99893282-100585889	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1039852	chr11:99901695-100610533	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv541152	chr11:99901695-100610533	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1043022	chr11:100387466-100610533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv832246	chr11:100426725-100606957	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100547400-100556400	Weak transcription	Placenta	Placenta
2	chr11:100547600-100557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:100548000-100557200	Weak transcription	K562	blood
4	chr11:100548800-100557000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:100551800-100557600	Weak transcription	Fetal Brain Male	brain
6	chr11:100552000-100556200	Weak transcription	Fetal Stomach	stomach
7	chr11:100552200-100555600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:100552200-100557000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:100552200-100557200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:100552200-100557200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:100552200-100557200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:100552200-100557200	Weak transcription	Fetal Intestine Small	intestine
13	chr11:100552200-100557200	Weak transcription	Fetal Muscle Leg	muscle
14	chr11:100552200-100557400	Weak transcription	Fetal Brain Female	brain
15	chr11:100552200-100557600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:100552400-100555600	Weak transcription	Adipose Nuclei	Adipose
17	chr11:100552400-100557400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:100552400-100557400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:100552600-100556400	Enhancers	GM12878-XiMat	blood
20	chr11:100552600-100557400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:100552600-100557400	Weak transcription	Dnd41	blood
22	chr11:100553000-100556200	Enhancers	HepG2	liver
23	chr11:100553000-100557400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:100553400-100555400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr11:100553400-100555800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr11:100553400-100556400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:100553400-100556800	Enhancers	Liver	Liver
28	chr11:100553400-100557400	Weak transcription	Primary T cells from cord blood	blood
29	chr11:100553600-100555600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr11:100553600-100556400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:100554000-100555400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr11:100554000-100555400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:100554200-100557200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:100554200-100557400	Weak transcription	Right Atrium	heart
35	chr11:100554400-100555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:100554400-100556600	Enhancers	HMEC	breast
37	chr11:100554400-100556800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:100554600-100556000	Bivalent Enhancer	Fetal Lung	lung
39	chr11:100554600-100556400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:100554600-100557600	Enhancers	Primary B cells from cord blood	blood
41	chr11:100554800-100555400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:100554800-100555400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr11:100554800-100555400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr11:100554800-100555800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:100554800-100555800	Enhancers	Brain Anterior Caudate	brain
46	chr11:100554800-100556600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:100554800-100556600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:100554800-100556600	Enhancers	Osteobl	bone
49	chr11:100554800-100556800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:100554800-100557600	Enhancers	Primary B cells from peripheral blood	blood

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