Variant report

Variant	rs4953617
Chromosome Location	chr2:48953209-48953210
allele	C/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	RAD21	chr2:48952770-48953220	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr2:48952834-48953611	K562	blood:	n/a	n/a
3	RAD21	chr2:48952877-48953304	HCT-116	colon:	n/a	n/a
4	CTCF	chr2:48952828-48953211	K562	blood:	n/a	n/a
5	RAD21	chr2:48952815-48953272	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr2:48952771-48953238	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48947110..48949799-chr2:48950949..48954085,3	K562	blood:
2	chr2:48947110..48950890-chr2:48950949..48954085,5	K562	blood:

Variant related genes	Relation type
LHCGR	TF binding region
ENSG00000138039	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1404057	1.00[CHD][hapmap]
rs1464728	1.00[CHD][hapmap]
rs1524149	1.00[CHD][hapmap]
rs1554613	1.00[CHD][hapmap]
rs2956355	1.00[CHD][hapmap]
rs4953611	1.00[CHD][hapmap]
rs6712571	1.00[CHD][hapmap]
rs6725834	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv817851	chr2:48941428-48973127	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48943400-48955400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:48943400-48956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:48945400-48955600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:48947000-48955400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:48947200-48956000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:48947400-48955800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:48947600-48956000	Weak transcription	Brain Anterior Caudate	brain
8	chr2:48947600-48956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:48947800-48955400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:48949800-48955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:48950000-48955800	Weak transcription	Fetal Stomach	stomach
12	chr2:48950600-48953800	Weak transcription	Fetal Lung	lung
13	chr2:48950600-48955200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:48950600-48960400	Weak transcription	Ovary	ovary
15	chr2:48950800-48959600	Weak transcription	Adipose Nuclei	Adipose
16	chr2:48951200-48954400	Weak transcription	NHDF-Ad	bronchial
17	chr2:48952600-48955800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:48952800-48956000	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:48953000-48953400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:48953000-48953400	Enhancers	Left Ventricle	heart
21	chr2:48953000-48953800	Enhancers	K562	blood
22	chr2:48953200-48954000	Weak transcription	Stomach Smooth Muscle	stomach

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