Variant report

Variant	rs277660
Chromosome Location	chr3:100033117-100033118
allele	A/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	POLR2A	chr3:100033049-100033245	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100031939..100034356-chr3:100427842..100429527,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D23	TF binding region
ENSG00000114354	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1214371	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2029162	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2178397	0.93[ASN][1000 genomes]
rs2316246	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs277637	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs277655	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs277656	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34547730	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35805111	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35939236	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36013739	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs384528	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3862050	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4928118	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55660654	0.98[ASN][1000 genomes]
rs57048357	0.87[AMR][1000 genomes]
rs6804963	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9810704	0.81[AFR][1000 genomes]
rs9968163	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
2	chr3:99980600-100053200	Weak transcription	Gastric	stomach
3	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
4	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
6	chr3:99998600-100033800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:100007000-100045000	Weak transcription	Lung	lung
8	chr3:100007800-100035800	Weak transcription	A549	lung
9	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
10	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:100014600-100042200	Weak transcription	Fetal Brain Male	brain
12	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:100018800-100035800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:100019000-100043200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:100019200-100038200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:100019600-100053000	Weak transcription	Colonic Mucosa	Colon
17	chr3:100019800-100034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:100020000-100038600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:100020600-100033600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:100020600-100053000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:100020600-100053000	Weak transcription	Hela-S3	cervix
22	chr3:100021200-100035600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:100021200-100036000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:100021800-100033400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:100021800-100052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:100021800-100053000	Weak transcription	Psoas Muscle	Psoas
27	chr3:100022000-100047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:100022000-100052800	Weak transcription	Pancreas	Pancrea
29	chr3:100025800-100038800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:100025800-100053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:100025800-100053000	Weak transcription	Right Ventricle	heart
32	chr3:100026000-100035600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:100026000-100038600	Weak transcription	HMEC	breast
34	chr3:100026000-100052600	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:100026000-100052800	Weak transcription	Thymus	Thymus
36	chr3:100026200-100038600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:100026400-100033200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:100026400-100034400	Weak transcription	Fetal Thymus	thymus
39	chr3:100026400-100035600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:100026400-100035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:100026400-100038400	Weak transcription	Ovary	ovary
42	chr3:100026400-100038600	Weak transcription	Brain Germinal Matrix	brain
43	chr3:100026400-100038600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:100026400-100038800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:100026400-100038800	Weak transcription	K562	blood
46	chr3:100026400-100045600	Weak transcription	HSMMtube	muscle
47	chr3:100026400-100052800	Weak transcription	NHEK	skin
48	chr3:100026400-100053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:100026600-100048600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr3:100026600-100052800	Weak transcription	Stomach Smooth Muscle	stomach

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