Variant report

Variant	rs2409084
Chromosome Location	chr12:49056787-49056788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49056323-49057495	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:49056685-49056854	MCF-7	breast:	n/a	n/a
3	FOS	chr12:49056764-49056874	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:49046686..49049905-chr12:49054030..49058402,3	K562	blood:
2	chr12:49052583..49059422-chr12:49071692..49076510,9	K562	blood:
3	chr12:49052650..49057544-chr12:49071692..49076123,6	K562	blood:
4	chr12:49054189..49057394-chr12:49060673..49063657,4	K562	blood:
5	chr12:49055891..49058972-chr12:49060822..49063197,4	K562	blood:
6	chr12:49055791..49059056-chr12:49060422..49062626,3	MCF-7	breast:
7	chr12:49049545..49052092-chr12:49054304..49056885,2	K562	blood:

No data

Variant related genes	Relation type
KANSL2	TF binding region
ENSG00000207313	Chromatin interaction
ENSG00000221491	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000206612	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10875851	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168620	1.00[ASN][1000 genomes]
rs11168659	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168660	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168661	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168664	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168667	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168680	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168690	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168691	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168692	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168693	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168694	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168695	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168699	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168700	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168701	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168708	1.00[ASN][1000 genomes]
rs11168715	1.00[ASN][1000 genomes]
rs11168717	1.00[ASN][1000 genomes]
rs11168718	1.00[ASN][1000 genomes]
rs11168719	1.00[ASN][1000 genomes]
rs11168722	1.00[ASN][1000 genomes]
rs11168727	1.00[ASN][1000 genomes]
rs11168781	1.00[ASN][1000 genomes]
rs11832160	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837643	1.00[ASN][1000 genomes]
rs12366919	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369279	1.00[ASN][1000 genomes]
rs17123362	1.00[ASN][1000 genomes]
rs17834622	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895994	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132370	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405363	1.00[ASN][1000 genomes]
rs55644947	1.00[ASN][1000 genomes]
rs56182935	1.00[ASN][1000 genomes]
rs61942011	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61942012	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942013	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942014	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942015	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942016	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942018	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942047	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942048	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942049	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942051	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942052	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942053	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61942058	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942059	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943193	1.00[ASN][1000 genomes]
rs61943194	1.00[ASN][1000 genomes]
rs6580694	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs7138342	1.00[ASN][1000 genomes]
rs7294389	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295027	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295138	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296987	1.00[ASN][1000 genomes]
rs7303113	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105786	1.00[ASN][1000 genomes]
rs74088163	1.00[ASN][1000 genomes]
rs7486636	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964801	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966343	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967175	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967542	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973954	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975102	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs7977935	1.00[ASN][1000 genomes]
rs7979508	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953673	1.00[ASN][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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1043220	chr12:49045458-49065987	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1052256	chr12:49048506-49065987	Genic enhancers Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	5 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	chr12:49036800-49072000	Strong transcription	Liver	Liver
2	chr12:49037800-49072400	Strong transcription	Placenta	Placenta
3	chr12:49038200-49070800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:49038400-49060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:49038800-49071800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:49039000-49072200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:49039400-49068800	Weak transcription	Right Atrium	heart
8	chr12:49039400-49071800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:49039800-49071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:49039800-49071000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:49040000-49057000	Strong transcription	Dnd41	blood
12	chr12:49040000-49059400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:49040000-49072600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:49040400-49060600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:49040400-49072800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:49041000-49071800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:49041200-49061200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:49041200-49068200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr12:49041600-49065200	Weak transcription	Stomach Mucosa	stomach
20	chr12:49041800-49065200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:49041800-49070800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:49041800-49071000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:49041800-49072400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:49041800-49073800	Strong transcription	Fetal Intestine Large	intestine
25	chr12:49042400-49056800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:49042400-49065200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:49042400-49072800	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:49042600-49064200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:49043800-49057600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr12:49043800-49068800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:49044000-49068200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:49044200-49057000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:49044200-49059800	Strong transcription	A549	lung
34	chr12:49044200-49071000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:49044200-49072400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:49044200-49072800	Strong transcription	Fetal Thymus	thymus
37	chr12:49044400-49057000	Strong transcription	NHEK	skin
38	chr12:49044400-49065200	Strong transcription	Osteobl	bone
39	chr12:49044400-49071000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:49044400-49071400	Strong transcription	Thymus	Thymus
41	chr12:49044400-49072400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:49044600-49072400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:49044800-49068000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:49044800-49071200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:49045000-49067600	Strong transcription	Left Ventricle	heart
46	chr12:49045000-49071600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:49045200-49057200	Strong transcription	NH-A	brain
48	chr12:49045200-49068200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:49045200-49069400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:49045200-49070400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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