Variant report

Variant	rs6544904
Chromosome Location	chr2:46847464-46847465
allele	C/T
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:8)
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	EGR1	chr2:46847363-46847549	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46845600..46848148-chr2:46860947..46862599,2	K562	blood:
2	chr2:46843822..46846111-chr2:46846206..46848342,2	K562	blood:
3	chr2:46846910..46848798-chr2:46875562..46877263,2	K562	blood:
4	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
5	chr2:46845764..46848148-chr2:46860387..46862849,3	K562	blood:
6	chr2:46842719..46845147-chr2:46846797..46849881,4	MCF-7	breast:
7	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:
8	chr2:46846051..46848798-chr2:46875763..46878074,2	K562	blood:

No data

Variant related genes	Relation type
PIGF	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1057899	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060656	1.00[ASN][1000 genomes]
rs11306	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1137748	1.00[ASN][1000 genomes]
rs11901678	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903907	0.87[ASN][1000 genomes]
rs13404342	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13406609	1.00[ASN][1000 genomes]
rs13410076	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376406	1.00[ASN][1000 genomes]
rs1456018	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035272	0.87[ASN][1000 genomes]
rs17035361	1.00[ASN][1000 genomes]
rs1809087	0.87[ASN][1000 genomes]
rs2276554	0.97[ASN][1000 genomes]
rs3213985	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768723	1.00[ASN][1000 genomes]
rs3768724	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4300884	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377377	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57134465	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57955462	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58101879	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58342271	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59183773	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59823825	0.87[ASN][1000 genomes]
rs60211996	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60738814	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61252474	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6544908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713104	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719813	1.00[ASN][1000 genomes]
rs6727471	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733143	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756134	1.00[ASN][1000 genomes]
rs68104662	0.93[ASN][1000 genomes]
rs72875696	0.87[ASN][1000 genomes]
rs7563577	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591561	0.87[ASN][1000 genomes]
rs7592446	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs962467	0.87[ASN][1000 genomes]
rs9808496	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
5	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
6	chr2:46845200-46847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:46845200-46850000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:46845200-46854000	Weak transcription	Colonic Mucosa	Colon
9	chr2:46845400-46854000	Weak transcription	Small Intestine	intestine
10	chr2:46845400-46858400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
12	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
14	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
15	chr2:46845600-46850000	Weak transcription	Fetal Heart	heart
16	chr2:46845600-46854800	Weak transcription	NHEK	skin
17	chr2:46845600-46868200	Weak transcription	Aorta	Aorta
18	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:46845800-46847800	Weak transcription	A549	lung
20	chr2:46845800-46849800	Weak transcription	HMEC	breast
21	chr2:46845800-46850000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:46846000-46849400	Strong transcription	Osteobl	bone
23	chr2:46846000-46854400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
25	chr2:46846200-46849000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:46846200-46849000	Strong transcription	Dnd41	blood
27	chr2:46846200-46849400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:46846200-46853400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:46846200-46855200	Strong transcription	Liver	Liver
30	chr2:46846200-46857400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:46846400-46853400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:46846400-46853600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:46846400-46853800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:46846400-46853800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:46846400-46853800	Strong transcription	Placenta	Placenta
36	chr2:46846400-46856000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:46846400-46857800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:46846600-46848800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:46846800-46848000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:46846800-46848600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:46846800-46848600	Strong transcription	Colon Smooth Muscle	Colon
42	chr2:46846800-46848600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:46846800-46848600	Strong transcription	Rectal Smooth Muscle	rectum
44	chr2:46846800-46848600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:46846800-46848600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:46846800-46848600	Strong transcription	Thymus	Thymus
47	chr2:46846800-46848600	Strong transcription	HSMMtube	muscle
48	chr2:46846800-46848600	Strong transcription	HUVEC	blood vessel
49	chr2:46846800-46848600	Strong transcription	NHLF	lung
50	chr2:46846800-46848800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links