Variant report

Variant	rs41273611
Chromosome Location	chr3:101401248-101401249
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	POLR2A	chr3:101400948-101401401	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:101398301-101401459	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:101401211-101401296	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:101395783-101401679	K562	blood:	n/a	n/a
5	POLR2A	chr3:101401215-101401429	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:101401021-101401465	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:101400243-101401358	K562	blood:	n/a	n/a
8	POLR2A	chr3:101394548-101402463	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:101400928-101401472	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:101398409-101401956	K562	blood:	n/a	n/a
11	POLR2A	chr3:101401141-101401464	HCT-116	colon:	n/a	n/a
12	POLR2A	chr3:101400207-101401434	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:101400160-101401630	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr3:101401144-101401423	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:101400958-101401309	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:101401240-101401400	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ZBTB11	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1078153	0.89[EUR][1000 genomes]
rs11924203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929578	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12491044	0.88[EUR][1000 genomes]
rs12696325	0.89[EUR][1000 genomes]
rs1426386	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1569071	0.89[EUR][1000 genomes]
rs3846092	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4234491	0.89[EUR][1000 genomes]
rs4683853	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683930	0.88[EUR][1000 genomes]
rs6763679	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6764700	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6768114	0.88[EUR][1000 genomes]
rs6768182	0.89[EUR][1000 genomes]
rs6774950	0.82[EUR][1000 genomes]
rs6779278	0.89[EUR][1000 genomes]
rs6779775	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6788864	0.89[EUR][1000 genomes]
rs6791803	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6794860	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6805496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806256	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72948053	0.88[EUR][1000 genomes]
rs7613194	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7618600	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7621062	0.89[EUR][1000 genomes]
rs7644519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645698	1.00[AMR][1000 genomes];0.96[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101396400-101402800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:101397000-101402400	Weak transcription	Fetal Brain Male	brain
3	chr3:101397000-101402600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:101397200-101402600	Weak transcription	Right Atrium	heart
5	chr3:101397200-101402600	Weak transcription	Right Ventricle	heart
6	chr3:101397200-101402800	Weak transcription	Fetal Heart	heart
7	chr3:101397400-101402000	Strong transcription	Fetal Intestine Small	intestine
8	chr3:101398400-101402000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:101398400-101402000	Strong transcription	Fetal Brain Female	brain
10	chr3:101398400-101402200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:101398400-101402600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:101398400-101402600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:101398400-101402800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:101398400-101403400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:101398600-101401400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:101398600-101401600	Strong transcription	A549	lung
17	chr3:101398600-101402200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:101398600-101402200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:101398600-101402200	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:101398600-101402200	Strong transcription	Hela-S3	cervix
21	chr3:101398600-101402600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr3:101398600-101402600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:101398600-101402600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:101398600-101402600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:101398600-101402600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:101398600-101402600	Strong transcription	Fetal Lung	lung
27	chr3:101398600-101402600	Strong transcription	Placenta	Placenta
28	chr3:101398600-101402600	Strong transcription	Fetal Thymus	thymus
29	chr3:101398600-101402600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:101398600-101402800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:101398600-101403000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:101398600-101403800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:101398800-101401400	Strong transcription	Gastric	stomach
34	chr3:101398800-101401400	Strong transcription	Lung	lung
35	chr3:101398800-101401400	Strong transcription	Thymus	Thymus
36	chr3:101398800-101401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:101398800-101401800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:101398800-101401800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:101398800-101401800	Strong transcription	Brain Angular Gyrus	brain
40	chr3:101398800-101401800	Strong transcription	Brain Germinal Matrix	brain
41	chr3:101398800-101401800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:101398800-101401800	Strong transcription	HSMMtube	muscle
43	chr3:101398800-101402000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:101398800-101402000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:101398800-101402000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr3:101398800-101402000	Strong transcription	Brain Substantia Nigra	brain
47	chr3:101398800-101402000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:101398800-101402000	Strong transcription	HUVEC	blood vessel
49	chr3:101398800-101402200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:101398800-101402200	Strong transcription	Fetal Stomach	stomach

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