Variant report

Variant	rs2241726
Chromosome Location	chr12:49444545-49444546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
2	chr12:49433492..49436536-chr12:49441197..49445190,3	MCF-7	breast:
3	chr12:49440399..49445270-chr12:49522815..49527186,6	K562	blood:
4	chr12:49435177..49437578-chr12:49443726..49445430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000200309	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10459221	0.89[ASN][1000 genomes]
rs10459232	0.89[ASN][1000 genomes]
rs1054442	0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10783299	0.92[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783300	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783301	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875908	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10875910	0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875911	0.84[ASN][1000 genomes]
rs10875912	0.83[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs10875913	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875914	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875915	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875917	0.89[ASN][1000 genomes]
rs10875918	0.89[ASN][1000 genomes]
rs11168822	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168827	0.96[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168838	0.92[ASN][1000 genomes]
rs11168839	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168850	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs1138908	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11614738	0.84[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12298884	0.85[ASN][1000 genomes]
rs12580349	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12821008	0.89[ASN][1000 genomes]
rs2117029	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293445	0.88[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293446	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304275	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs34436857	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3741619	0.89[ASW][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs3782357	0.96[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580698	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6580699	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs7296288	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7300136	0.89[ASN][1000 genomes]
rs7969091	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs876333	0.88[ASN][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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2241726	RHEBL1	cis	cerebellum	SCAN
rs2241726	DDN	cis	Muscle Skeletal	GTEx
rs2241726	RHEBL1	cis	parietal	SCAN
rs2241726	NCKAP5L	cis	parietal	SCAN
rs2241726	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs2241726	ENSG00000167550	cis	multi-tissue	Pritchard
rs2241726	RP11-386G11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49413000-49453400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49413400-49449000	Strong transcription	Fetal Intestine Small	intestine
3	chr12:49413800-49449200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:49414200-49449000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:49414400-49448800	Strong transcription	Colonic Mucosa	Colon
6	chr12:49414400-49449000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:49414400-49449000	Strong transcription	Brain Cingulate Gyrus	brain
8	chr12:49414400-49449000	Strong transcription	Brain Germinal Matrix	brain
9	chr12:49414400-49449200	Strong transcription	Fetal Stomach	stomach
10	chr12:49414400-49449200	Strong transcription	Fetal Thymus	thymus
11	chr12:49414400-49449200	Strong transcription	Thymus	Thymus
12	chr12:49414400-49449400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:49414400-49449400	Strong transcription	Fetal Intestine Large	intestine
14	chr12:49414400-49449800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:49414600-49448600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:49414600-49448600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:49414600-49448600	Strong transcription	Adipose Nuclei	Adipose
18	chr12:49414600-49448800	Strong transcription	Ovary	ovary
19	chr12:49414600-49449000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr12:49414600-49449000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:49414600-49449000	Strong transcription	Primary T cells from cord blood	blood
22	chr12:49414600-49449400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:49414600-49449600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:49414600-49449800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:49414800-49447200	Strong transcription	Dnd41	blood
26	chr12:49414800-49448200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:49414800-49449200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:49414800-49449200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:49414800-49449400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:49414800-49449400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:49415000-49449000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:49415000-49449000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:49415000-49449000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr12:49415200-49448600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:49415200-49448600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:49415200-49448800	Strong transcription	Liver	Liver
37	chr12:49415200-49449600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:49415400-49449000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:49415400-49449200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr12:49415600-49449000	Strong transcription	Fetal Lung	lung
41	chr12:49417800-49449200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:49417800-49449400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:49420600-49449000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:49424800-49448000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:49424800-49448000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:49424800-49448800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:49425600-49448600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:49425600-49449400	Weak transcription	Right Atrium	heart
49	chr12:49427800-49449400	Strong transcription	Brain Substantia Nigra	brain
50	chr12:49428000-49448400	Strong transcription	Brain Hippocampus Middle	brain

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