Variant report

Variant	rs11249672
Chromosome Location	chr5:179562986-179562987
allele	A/C
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	ELF1	chr5:179561913-179563218	MCF-7	breast:	n/a	n/a
2	NR2F2	chr5:179561974-179563355	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
RASGEF1C	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10067359	1.00[EUR][1000 genomes]
rs10072480	1.00[EUR][1000 genomes]
rs10903249	1.00[EUR][1000 genomes]
rs2069332	1.00[EUR][1000 genomes]
rs4700715	1.00[EUR][1000 genomes]
rs4700878	1.00[EUR][1000 genomes]
rs4700879	1.00[EUR][1000 genomes]
rs6601084	1.00[EUR][1000 genomes]
rs6601085	1.00[EUR][1000 genomes]
rs6878491	1.00[EUR][1000 genomes]
rs6878835	1.00[EUR][1000 genomes]
rs6882752	1.00[EUR][1000 genomes]
rs6882917	1.00[EUR][1000 genomes]
rs6897364	1.00[EUR][1000 genomes]
rs7707107	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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv1033460	chr5:179526789-179565253	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1020038	chr5:179526789-179566589	Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv883287	chr5:179526789-179584778	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv883288	chr5:179537727-179608656	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv1030036	chr5:179543546-179610871	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv830562	chr5:179555313-179622441	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv3392751	chr5:179560495-179563780	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179555400-179571000	Weak transcription	Right Atrium	heart
2	chr5:179556800-179566600	Weak transcription	Brain Angular Gyrus	brain
3	chr5:179559600-179565800	Weak transcription	Fetal Brain Female	brain
4	chr5:179561800-179563000	Enhancers	Osteobl	bone
5	chr5:179561800-179563200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:179561800-179563200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:179562000-179563200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:179562000-179563200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr5:179562000-179564200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:179562200-179563000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:179562200-179563200	Enhancers	Fetal Muscle Leg	muscle
12	chr5:179562200-179564000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:179562600-179563200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:179562600-179565000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:179562600-179567000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:179562800-179566000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:179562800-179566600	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:179562800-179566800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:179562800-179567000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:179562800-179567400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links