Variant report

Variant	rs2230149
Chromosome Location	chr3:49845526-49845527
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	chr3:49845330-49845829	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:49844762-49845731	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:49845478-49845646	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:49845136-49845945	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49844984-49845766	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:49844980-49845934	GM12892	blood:	n/a	n/a
7	MTA3	chr3:49839849-49845759	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:49845370-49845631	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49839942-49845851	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:49844959-49846010	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:
2	chr3:49838468..49840938-chr3:49845462..49847993,2	MCF-7	breast:

Variant related genes	Relation type
MIR5193	TF binding region
UBA7	TF binding region
ENSG00000185614	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs6800591	1.00[EUR][1000 genomes]
rs6801718	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6806073	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49841400-49845800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
2	chr3:49841400-49845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr3:49841400-49846400	Weak transcription	Ovary	ovary
4	chr3:49841400-49847000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:49841600-49845600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:49841600-49845800	Enhancers	Dnd41	blood
7	chr3:49841600-49846000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr3:49841600-49846200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:49841600-49850400	Weak transcription	Small Intestine	intestine
10	chr3:49841800-49845600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:49841800-49845600	Enhancers	Left Ventricle	heart
12	chr3:49841800-49845800	Enhancers	Right Atrium	heart
13	chr3:49842000-49845800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:49842000-49845800	Enhancers	Right Ventricle	heart
15	chr3:49842000-49850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:49842200-49845600	Enhancers	Lung	lung
17	chr3:49842200-49846600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:49842600-49845600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr3:49842600-49846000	Enhancers	NHEK	skin
20	chr3:49842800-49846000	Enhancers	Esophagus	oesophagus
21	chr3:49843000-49845600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:49843400-49845600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:49843400-49845800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:49843400-49845800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:49843400-49845800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:49843400-49846000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:49843400-49846200	Enhancers	Fetal Heart	heart
28	chr3:49843400-49846400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:49843600-49845600	Enhancers	HUVEC	blood vessel
31	chr3:49843600-49846000	Genic enhancers	Fetal Intestine Small	intestine
32	chr3:49843600-49846000	Enhancers	Fetal Muscle Leg	muscle
33	chr3:49843600-49846400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:49843600-49846400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:49843600-49846400	Weak transcription	Aorta	Aorta
36	chr3:49843600-49846400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:49843600-49846400	Weak transcription	Osteobl	bone
38	chr3:49843600-49846600	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:49843600-49846800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:49843600-49850400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:49843600-49850600	Weak transcription	HSMM	muscle
42	chr3:49843600-49850800	Weak transcription	Psoas Muscle	Psoas
43	chr3:49844000-49845600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:49844000-49845600	Enhancers	Fetal Kidney	kidney
45	chr3:49844000-49845800	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr3:49844000-49847600	Genic enhancers	Fetal Thymus	thymus
47	chr3:49844000-49850200	Weak transcription	NHDF-Ad	bronchial
48	chr3:49844200-49845600	Enhancers	HMEC	breast
49	chr3:49844200-49846800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:49844200-49846800	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links