Variant report

Variant	rs3003899
Chromosome Location	chr1:222014731-222014732
allele	A/C
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	PRDM1	chr1:222014626-222014979	Hela-S3	cervix:	n/a	chr1:222014821-222014836
2	POLR2A	chr1:222014325-222014762	K562	blood:	n/a	n/a
3	POLR2A	chr1:222014546-222015074	HL-60	blood:	n/a	n/a
4	MXI1	chr1:222014664-222014795	GM12878	blood:	n/a	n/a
5	WRNIP1	chr1:222012674-222014895	GM12878	blood:	n/a	n/a
6	CEBPB	chr1:222014726-222014973	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr1:222014518-222014884	Hela-S3	cervix:	n/a	n/a
8	EP300	chr1:222014713-222014913	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000227925	TF binding region
RNU6-403P	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10495180	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17010904	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4846729	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222000600-222019000	Weak transcription	Lung	lung
2	chr1:222005800-222019000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:222008800-222018800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:222010400-222015200	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:222010600-222015000	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:222011400-222015000	Enhancers	HUVEC	blood vessel
7	chr1:222011600-222015600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:222011600-222018800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:222011800-222015600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:222011800-222016000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:222012600-222015000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:222012600-222015000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:222012600-222015000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:222012600-222015000	Enhancers	Hela-S3	cervix
15	chr1:222012600-222015000	Enhancers	HMEC	breast
16	chr1:222012600-222015000	Enhancers	NHEK	skin
17	chr1:222012600-222015400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:222012600-222015600	Enhancers	HSMMtube	muscle
19	chr1:222012600-222015800	Enhancers	HSMM	muscle
20	chr1:222012800-222014800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:222012800-222014800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:222012800-222015400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:222012800-222015600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:222012800-222015600	Enhancers	NHDF-Ad	bronchial
25	chr1:222013000-222015600	Enhancers	NHLF	lung
26	chr1:222013000-222015800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:222013000-222015800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:222013200-222015200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:222013400-222015000	Enhancers	Fetal Muscle Leg	muscle
30	chr1:222013600-222014800	Enhancers	GM12878-XiMat	blood
31	chr1:222013600-222018800	Weak transcription	NH-A	brain
32	chr1:222013800-222015400	Enhancers	Fetal Lung	lung
33	chr1:222014000-222015400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr1:222014000-222015600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:222014000-222018600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:222014200-222019000	Weak transcription	A549	lung
37	chr1:222014400-222022000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:222014600-222015000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:222014600-222018800	Weak transcription	Stomach Mucosa	stomach
40	chr1:222014600-222019000	Weak transcription	Esophagus	oesophagus
41	chr1:222014600-222019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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