Variant report

Variant	rs6545061
Chromosome Location	chr2:48952574-48952575
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	RCOR1	chr2:48952531-48952643	K562	blood:	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: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10495957	0.89[ASN][1000 genomes]
rs10495958	0.81[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12996684	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs13013236	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13017840	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17326446	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4366951	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516485	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4574159	0.82[CEU][hapmap]
rs68073206	1.00[ASN][1000 genomes]
rs7579411	0.85[GIH][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	chr2:48943200-48953000	Weak transcription	K562	blood
2	chr2:48943400-48955400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:48943400-48956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:48945400-48955600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:48947000-48955400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:48947200-48956000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:48947400-48955800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:48947600-48956000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:48947600-48956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:48947800-48955400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:48949800-48955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:48950000-48955800	Weak transcription	Fetal Stomach	stomach
13	chr2:48950600-48953800	Weak transcription	Fetal Lung	lung
14	chr2:48950600-48955200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:48950600-48960400	Weak transcription	Ovary	ovary
16	chr2:48950800-48959600	Weak transcription	Adipose Nuclei	Adipose
17	chr2:48951200-48954400	Weak transcription	NHDF-Ad	bronchial
18	chr2:48951600-48952600	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:48951800-48952800	Enhancers	Brain Hippocampus Middle	brain
20	chr2:48951800-48953000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:48952400-48953000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:48952400-48953200	Enhancers	Stomach Smooth Muscle	stomach

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