Variant report

Variant	rs4596023
Chromosome Location	chr2:48955683-48955684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48955353..48957599-chr2:48959365..48961603,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11887058	0.83[ASN][1000 genomes]
rs11892719	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs11897846	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs12998409	0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs4074647	0.81[CEU][hapmap]
rs4074648	0.81[CEU][hapmap]
rs4319975	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4953618	0.82[ASN][1000 genomes]
rs4953619	0.85[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4953620	0.80[ASN][1000 genomes]
rs4953625	0.91[MEX][hapmap];0.82[YRI][hapmap]
rs7561278	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7563144	0.91[MEX][hapmap]
rs9798043	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4596023	LHCGR	cis	Esophagus Muscularis	GTEx
rs4596023	LHCGR	cis	Thyroid	GTEx
rs4596023	BEX1	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48943400-48956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:48947200-48956000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:48947400-48955800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48947600-48956000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:48947600-48956600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:48950000-48955800	Weak transcription	Fetal Stomach	stomach
7	chr2:48950600-48960400	Weak transcription	Ovary	ovary
8	chr2:48950800-48959600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:48952600-48955800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:48952800-48956000	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:48953400-48956200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:48954000-48957000	Enhancers	Stomach Smooth Muscle	stomach
13	chr2:48955000-48956600	Enhancers	Fetal Heart	heart
14	chr2:48955200-48957000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:48955200-48957200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:48955400-48955800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:48955400-48955800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:48955400-48956000	Enhancers	Colon Smooth Muscle	Colon
19	chr2:48955400-48956800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:48955400-48957800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:48955400-48958000	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:48955400-48958000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:48955600-48956400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:48955600-48957800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:48955600-48958000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:48955600-48960400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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