Variant report

Variant	rs2028146
Chromosome Location	chr2:209133048-209133049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr2:209133014-209133434	PBDE	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:209121994..209124234-chr2:209131369..209133621,2	MCF-7	breast:
2	chr2:209104332..209106656-chr2:209130862..209133286,2	MCF-7	breast:
3	chr2:209111341..209112901-chr2:209132498..209134029,2	K562	blood:
4	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
5	chr2:209129669..209131681-chr2:209132251..209135245,2	K562	blood:
6	chr2:209118313..209121811-chr2:209130870..209135068,6	MCF-7	breast:
7	chr2:209129671..209132812-chr2:209132994..209136144,5	MCF-7	breast:

No data

Variant related genes	Relation type
IDH1	TF binding region
ENSG00000138413	Chromatin interaction
ENSG00000231908	Chromatin interaction
ENSG00000115020	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10171006	1.00[EUR][1000 genomes]
rs10175739	1.00[EUR][1000 genomes]
rs10186531	1.00[EUR][1000 genomes]
rs10197958	1.00[EUR][1000 genomes]
rs10201702	1.00[EUR][1000 genomes]
rs10208004	1.00[EUR][1000 genomes]
rs10210393	1.00[EUR][1000 genomes]
rs10804168	1.00[EUR][1000 genomes]
rs10932256	1.00[EUR][1000 genomes]
rs10932259	1.00[EUR][1000 genomes]
rs11677618	1.00[EUR][1000 genomes]
rs11691208	1.00[EUR][1000 genomes]
rs11695873	1.00[EUR][1000 genomes]
rs12185547	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12465862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12478198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12479282	1.00[EUR][1000 genomes]
rs12617521	1.00[EUR][1000 genomes]
rs12618837	1.00[EUR][1000 genomes]
rs12621871	1.00[EUR][1000 genomes]
rs12623816	1.00[EUR][1000 genomes]
rs12694105	1.00[EUR][1000 genomes]
rs12694109	1.00[EUR][1000 genomes]
rs13394932	0.86[AFR][1000 genomes]
rs1370370	1.00[EUR][1000 genomes]
rs1437414	1.00[EUR][1000 genomes]
rs1446320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1446321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1465803	1.00[EUR][1000 genomes]
rs1465804	1.00[EUR][1000 genomes]
rs1529979	1.00[EUR][1000 genomes]
rs1561240	1.00[EUR][1000 genomes]
rs16840898	1.00[EUR][1000 genomes]
rs16840910	1.00[EUR][1000 genomes]
rs16840936	1.00[EUR][1000 genomes]
rs1838794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1838795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1838796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1866044	1.00[EUR][1000 genomes]
rs1866045	1.00[EUR][1000 genomes]
rs2043720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2044457	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2118296	1.00[EUR][1000 genomes]
rs2118297	1.00[EUR][1000 genomes]
rs2304544	1.00[EUR][1000 genomes]
rs2363463	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2363468	1.00[EUR][1000 genomes]
rs2363469	1.00[EUR][1000 genomes]
rs2363579	1.00[EUR][1000 genomes]
rs2885785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885786	1.00[EUR][1000 genomes]
rs4673385	1.00[EUR][1000 genomes]
rs4673386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4673388	0.96[AFR][1000 genomes]
rs4673390	1.00[EUR][1000 genomes]
rs4673395	1.00[EUR][1000 genomes]
rs4675745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4675747	1.00[EUR][1000 genomes]
rs4675750	1.00[EUR][1000 genomes]
rs4675754	1.00[EUR][1000 genomes]
rs4675755	1.00[EUR][1000 genomes]
rs57553077	1.00[EUR][1000 genomes]
rs57797425	1.00[EUR][1000 genomes]
rs6435436	1.00[EUR][1000 genomes]
rs6435437	1.00[EUR][1000 genomes]
rs6435441	1.00[EUR][1000 genomes]
rs6435443	1.00[EUR][1000 genomes]
rs6435444	1.00[EUR][1000 genomes]
rs6435445	1.00[EUR][1000 genomes]
rs6435446	1.00[EUR][1000 genomes]
rs6435450	1.00[EUR][1000 genomes]
rs6705163	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6708926	1.00[EUR][1000 genomes]
rs6711933	1.00[EUR][1000 genomes]
rs6713477	1.00[EUR][1000 genomes]
rs6718402	1.00[EUR][1000 genomes]
rs6733607	1.00[EUR][1000 genomes]
rs6734963	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6742461	1.00[EUR][1000 genomes]
rs6751982	1.00[EUR][1000 genomes]
rs6754478	1.00[AFR][1000 genomes]
rs7564882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7569723	1.00[EUR][1000 genomes]
rs7574324	1.00[EUR][1000 genomes]
rs7576852	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7580715	1.00[EUR][1000 genomes]
rs7581075	1.00[EUR][1000 genomes]
rs7605498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs893253	1.00[EUR][1000 genomes]
rs893255	1.00[EUR][1000 genomes]
rs893256	1.00[EUR][1000 genomes]
rs9283521	1.00[EUR][1000 genomes]
rs934712	1.00[EUR][1000 genomes]
rs934714	1.00[EUR][1000 genomes]
rs959855	1.00[EUR][1000 genomes]
rs976247	1.00[EUR][1000 genomes]
rs994696	1.00[EUR][1000 genomes]
rs994697	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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr2:209130200-209133400	Active TSS	K562	blood
2	chr2:209130400-209133200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:209131600-209133200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:209131600-209133200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:209131600-209134400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:209131800-209134400	Enhancers	Small Intestine	intestine
7	chr2:209131800-209143200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:209132000-209133200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:209132000-209133200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr2:209132000-209133200	Enhancers	Brain Substantia Nigra	brain
11	chr2:209132000-209133400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:209132000-209133400	Enhancers	Fetal Muscle Trunk	muscle
13	chr2:209132000-209134400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:209132000-209134600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:209132000-209134600	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:209132000-209134600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:209132000-209134600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:209132200-209133200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:209132200-209133200	Enhancers	Fetal Lung	lung
20	chr2:209132200-209133200	Enhancers	Fetal Stomach	stomach
21	chr2:209132200-209133200	Enhancers	NH-A	brain
22	chr2:209132200-209133600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:209132200-209133800	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr2:209132200-209134200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:209132200-209134400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:209132200-209134600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:209132200-209134800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:209132200-209134800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:209132200-209138200	Weak transcription	HSMMtube	muscle
30	chr2:209132200-209144800	Weak transcription	Aorta	Aorta
31	chr2:209132400-209133200	Enhancers	Brain Hippocampus Middle	brain
32	chr2:209132400-209133200	Enhancers	Fetal Brain Female	brain
33	chr2:209132400-209133200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:209132400-209133600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:209132400-209133800	Flanking Active TSS	Dnd41	blood
36	chr2:209132400-209134000	Enhancers	Primary T cells from cord blood	blood
37	chr2:209132400-209134400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:209132400-209134800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:209132600-209133200	Enhancers	Osteobl	bone
40	chr2:209132600-209133400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:209132600-209133600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:209132600-209133600	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:209132600-209134000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:209132600-209134000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:209132600-209134000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:209132600-209134000	Enhancers	Brain Germinal Matrix	brain
47	chr2:209132600-209134200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:209132600-209134200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:209132600-209134400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:209132600-209134400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links