Variant report

Variant	rs55936680
Chromosome Location	chr3:24540860-24540861
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	E2F6	chr3:24540792-24541302	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24534014..24541118-chr3:24556364..24565705,22	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1D2-1	chr3:24540116-24540865	ENSG00000228791.3

Variant related genes	Relation type
THRB	TF binding region
ENSG00000265028	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs55661339	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56035340	1.00[AMR][1000 genomes]
rs61078139	1.00[AMR][1000 genomes]
rs73823333	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73823341	1.00[AMR][1000 genomes]
rs73823344	1.00[AMR][1000 genomes]
rs73823346	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73823350	1.00[AMR][1000 genomes]
rs73823351	1.00[AFR][1000 genomes]
rs73823353	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73823354	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73823355	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24537400-24541800	Weak transcription	HSMM	muscle
2	chr3:24537400-24546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:24537600-24542000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:24537800-24544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:24538000-24541600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:24538000-24542000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:24538000-24543600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:24538200-24541200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:24538200-24542200	Weak transcription	NHEK	skin
10	chr3:24538200-24542400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:24538200-24547000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:24538200-24552000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:24538200-24560600	Weak transcription	Aorta	Aorta
14	chr3:24538400-24544200	Weak transcription	HMEC	breast
15	chr3:24538400-24549000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:24538800-24541000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr3:24538800-24541000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:24539000-24541000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:24539000-24544400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:24539000-24547400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:24539000-24560200	Weak transcription	HepG2	liver
22	chr3:24539200-24541000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:24539600-24541000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr3:24539800-24543800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:24540000-24541000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:24540200-24541000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:24540200-24541000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:24540200-24541400	Enhancers	HSMMtube	muscle
29	chr3:24540400-24541000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:24540400-24541000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:24540400-24543600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:24540400-24543600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:24540400-24544200	Weak transcription	Fetal Intestine Small	intestine
34	chr3:24540400-24544200	Weak transcription	K562	blood
35	chr3:24540600-24541200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:24540600-24549000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:24540800-24541600	Enhancers	Stomach Mucosa	stomach

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