Variant report

Variant	rs9812673
Chromosome Location	chr3:42637545-42637546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42637099-42637669	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:42636237-42639709	K562	blood:	n/a	n/a
3	POLR2A	chr3:42637152-42637629	K562	blood:	n/a	n/a
4	POLR2A	chr3:42636950-42639278	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:42637462-42637868	HepG2	liver:	n/a	n/a
6	TAL1	chr3:42637217-42637570	K562	blood:	n/a	n/a
7	GATA2	chr3:42637152-42637572	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42631664..42634178-chr3:42636385..42639345,6	MCF-7	breast:
3	chr3:42603400..42605797-chr3:42635471..42638332,2	MCF-7	breast:
4	chr3:42632553..42639930-chr3:42692933..42696882,8	K562	blood:

No data

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000230084	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10154957	1.00[AMR][1000 genomes]
rs13320598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13325536	1.00[AMR][1000 genomes]
rs28508060	1.00[AMR][1000 genomes]
rs28549046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs580447	1.00[AMR][1000 genomes]
rs58273990	1.00[AMR][1000 genomes]
rs9812538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822273	1.00[AMR][1000 genomes]
rs9832720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9853946	1.00[AMR][1000 genomes]
rs9855071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869491	1.00[AMR][1000 genomes]
rs9876937	1.00[AMR][1000 genomes]
rs9884030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9985232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42641200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:42633400-42641200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:42633400-42641200	Weak transcription	HSMMtube	muscle
6	chr3:42633400-42641400	Weak transcription	Ovary	ovary
7	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
8	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
9	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
12	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
13	chr3:42633600-42637600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:42633600-42638000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:42633600-42639200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:42633600-42639400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:42633600-42641200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:42633600-42641200	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:42633600-42641200	Weak transcription	Fetal Kidney	kidney
20	chr3:42633600-42641200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:42633600-42641200	Weak transcription	Right Atrium	heart
22	chr3:42633600-42641200	Weak transcription	NHEK	skin
23	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
26	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
29	chr3:42633800-42638600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:42633800-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:42633800-42641200	Weak transcription	Brain Germinal Matrix	brain
32	chr3:42634000-42641200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:42634000-42641600	Weak transcription	Lung	lung
34	chr3:42634200-42638800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:42634400-42641200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:42634600-42641200	Weak transcription	Fetal Brain Male	brain
37	chr3:42634800-42638000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:42634800-42638200	Strong transcription	Fetal Thymus	thymus
39	chr3:42635000-42637600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:42635000-42637600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr3:42635000-42637600	Strong transcription	Liver	Liver
42	chr3:42635000-42637600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:42635000-42638600	Strong transcription	Primary B cells from cord blood	blood
44	chr3:42635000-42638600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:42635000-42639400	Strong transcription	HSMM	muscle
46	chr3:42635000-42639600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:42635200-42637600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:42635200-42638600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:42635200-42638800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:42635400-42638000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links