Variant report

Variant	rs1919590
Chromosome Location	chr3:119160423-119160424
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	chr3:119160205-119160639	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:119160393-119160641	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:119159981-119160748	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:119159768-119160655	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:119160389-119160803	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:119159440-119163995	K562	blood:	n/a	n/a
7	POLR2A	chr3:119159665-119160972	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:119160388-119160858	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119159984..119162749-chr3:119216871..119219085,2	MCF-7	breast:

Variant related genes	Relation type
TMEM39A	TF binding region
ENSG00000272662	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060569	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13080905	0.98[ASN][1000 genomes]
rs1797839	0.86[ASN][1000 genomes]
rs1900742	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919586	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967621	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976919	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2030816	0.85[AMR][1000 genomes]
rs2177812	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732413	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814397	0.86[ASN][1000 genomes]
rs4687855	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687860	0.98[ASN][1000 genomes]
rs4688005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688007	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688008	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688012	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688014	0.85[ASN][1000 genomes]
rs6414282	0.96[ASN][1000 genomes]
rs6414283	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438528	0.98[ASN][1000 genomes]
rs6438529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438530	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438531	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438535	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6777535	0.98[ASN][1000 genomes]
rs6778945	0.88[ASN][1000 genomes]
rs6794822	0.96[ASN][1000 genomes]
rs6796970	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727905	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430798	0.98[ASN][1000 genomes]
rs7621259	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628626	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7630587	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642502	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289129	0.98[ASN][1000 genomes]
rs9809155	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836326	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836627	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850447	0.88[ASN][1000 genomes]
rs9867768	0.88[ASN][1000 genomes]
rs9873196	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9874480	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877854	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119147000-119179000	Strong transcription	Osteobl	bone
2	chr3:119147200-119180400	Weak transcription	Stomach Mucosa	stomach
3	chr3:119147400-119179200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:119148000-119162200	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:119148800-119175400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:119148800-119180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:119149200-119161600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr3:119149400-119179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:119149400-119181000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:119149400-119181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:119149600-119172600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:119150000-119162000	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:119150200-119179000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:119150400-119160600	Strong transcription	Liver	Liver
15	chr3:119150400-119160800	Strong transcription	GM12878-XiMat	blood
16	chr3:119150400-119180200	Strong transcription	Fetal Intestine Large	intestine
17	chr3:119150600-119175400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:119150600-119180800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:119151000-119160800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119151000-119165000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:119152000-119178000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:119152000-119179800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:119152200-119178800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:119152200-119179400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:119152800-119161800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:119154000-119181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:119154400-119171400	Strong transcription	Fetal Stomach	stomach
28	chr3:119156000-119164200	Weak transcription	Psoas Muscle	Psoas
29	chr3:119156200-119163800	Weak transcription	Small Intestine	intestine
30	chr3:119156400-119165400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:119156800-119163800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:119156800-119164400	Weak transcription	HMEC	breast
33	chr3:119156800-119165000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:119157000-119160600	Weak transcription	HUVEC	blood vessel
35	chr3:119157000-119161400	Weak transcription	HSMMtube	muscle
36	chr3:119157000-119162000	Weak transcription	NHLF	lung
37	chr3:119157000-119163400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:119157000-119163400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:119157000-119163600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:119157000-119163800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:119157000-119163800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:119157000-119163800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:119157000-119163800	Weak transcription	Colonic Mucosa	Colon
44	chr3:119157000-119163800	Weak transcription	Gastric	stomach
45	chr3:119157000-119164200	Weak transcription	Pancreas	Pancrea
46	chr3:119157000-119164600	Weak transcription	Lung	lung
47	chr3:119157000-119164800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:119157000-119164800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:119157000-119165000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:119157000-119165000	Weak transcription	Spleen	Spleen

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