Variant report

Variant	rs12280935
Chromosome Location	chr11:100557421-100557422
allele	C/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	POU5F1	chr11:100557066-100557455	H1-hESC	embryonic stem cell:	n/a	chr11:100557331-100557345 chr11:100557331-100557345 chr11:100557332-100557346 chr11:100557331-100557345
2	TCF12	chr11:100557175-100557428	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF263	chr11:100557279-100558877	HEK293-T-REx	kidney:	n/a	chr11:100558219-100558228
4	POLR2A	chr11:100557227-100558736	H1-hESC	embryonic stem cell:	n/a	n/a
5	BACH1	chr11:100557257-100558831	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:100557273-100557520	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:100557265-100558827	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr11:100557068-100557588	H1-hESC	embryonic stem cell:	n/a	chr11:100557422-100557436
9	CHD2	chr11:100557298-100558225	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr11:100557197-100559182	H1-hESC	embryonic stem cell:	n/a	chr11:100557995-100558006 chr11:100557801-100557812
11	MAFK	chr11:100557231-100557540	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr11:100557044-100558940	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr11:100557159-100557491	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr11:100557211-100558185	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr11:100557304-100558833	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr11:100557196-100558787	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ARHGAP42	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10160326	0.85[ASN][1000 genomes]
rs10160408	0.85[ASN][1000 genomes]
rs10160533	0.85[ASN][1000 genomes]
rs10160586	0.85[ASN][1000 genomes]
rs10160729	0.85[ASN][1000 genomes]
rs1021794	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs10895006	0.83[ASN][1000 genomes]
rs10895007	0.85[ASN][1000 genomes]
rs10895008	0.85[ASN][1000 genomes]
rs11224376	0.83[ASN][1000 genomes]
rs11224377	0.83[ASN][1000 genomes]
rs11224378	0.85[ASN][1000 genomes]
rs11224379	0.85[ASN][1000 genomes]
rs11224380	0.83[ASN][1000 genomes]
rs11224381	0.83[ASN][1000 genomes]
rs11224382	0.85[ASN][1000 genomes]
rs11224387	0.85[ASN][1000 genomes]
rs11224389	0.85[ASN][1000 genomes]
rs11224390	0.83[CHB][hapmap]
rs4754693	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6590807	0.85[ASN][1000 genomes]
rs6590808	0.85[ASN][1000 genomes]
rs7107791	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs73573308	0.83[ASN][1000 genomes]
rs7928871	0.82[EUR][1000 genomes]
rs7929942	0.85[ASN][1000 genomes]
rs7938601	0.83[EUR][1000 genomes]
rs7947643	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs7952198	0.84[ASN][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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100547600-100557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:100551800-100557600	Weak transcription	Fetal Brain Male	brain
3	chr11:100552200-100557600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr11:100554600-100557600	Enhancers	Primary B cells from cord blood	blood
5	chr11:100554800-100557600	Enhancers	Primary B cells from peripheral blood	blood
6	chr11:100555000-100557600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr11:100555000-100557600	Enhancers	Colon Smooth Muscle	Colon
8	chr11:100555000-100557600	Enhancers	Stomach Mucosa	stomach
9	chr11:100555000-100557600	Enhancers	NHLF	lung
10	chr11:100555600-100557600	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:100555600-100557600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:100555600-100557600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:100556000-100557600	Weak transcription	Brain Germinal Matrix	brain
14	chr11:100556000-100557600	Enhancers	NHEK	skin
15	chr11:100556200-100557600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:100556400-100557600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:100556400-100557600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:100556600-100557600	Weak transcription	HMEC	breast
19	chr11:100556600-100558000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:100556800-100557600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:100557000-100560000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr11:100557200-100557600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr11:100557200-100557600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr11:100557200-100557600	Enhancers	Fetal Intestine Small	intestine
25	chr11:100557200-100559000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:100557200-100559600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr11:100557200-100559600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr11:100557200-100559600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr11:100557200-100559600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr11:100557200-100559800	Active TSS	Fetal Kidney	kidney
31	chr11:100557200-100560600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:100557400-100557600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:100557400-100557600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:100557400-100557600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:100557400-100557600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr11:100557400-100557600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:100557400-100557600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:100557400-100557600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:100557400-100557600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:100557400-100557600	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr11:100557400-100557600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:100557400-100557600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:100557400-100557600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:100557400-100557600	Flanking Active TSS	Liver	Liver
45	chr11:100557400-100557600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr11:100557400-100557600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:100557400-100557600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr11:100557400-100557600	Enhancers	Fetal Brain Female	brain
49	chr11:100557400-100557600	Bivalent/Poised TSS	Fetal Lung	lung
50	chr11:100557400-100557600	Flanking Active TSS	Fetal Stomach	stomach

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