Variant report

Variant	rs1143758
Chromosome Location	chr12:67708543-67708544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:67707079..67709730-chr12:67721053..67723374,2	K562	blood:
2	chr12:67707980..67709583-chr12:67712739..67715234,2	K562	blood:
3	chr12:67708479..67710797-chr12:67718354..67720777,2	MCF-7	breast:
4	chr12:67708442..67711026-chr12:67711731..67713764,2	MCF-7	breast:
5	chr12:67708053..67712275-chr12:67717926..67720355,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYRK2-3	chr12:67708478-67708952	ENSG00000247008

No data

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1066387	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1066388	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1066394	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1066395	1.00[AFR][1000 genomes]
rs10784625	0.90[CEU][hapmap]
rs1082701	1.00[AFR][1000 genomes]
rs1082702	1.00[AFR][1000 genomes]
rs1082708	0.94[AFR][1000 genomes]
rs1082709	0.94[AFR][1000 genomes]
rs1082711	0.97[AFR][1000 genomes]
rs11176678	0.90[CEU][hapmap]
rs1143947	0.94[AFR][1000 genomes]
rs1143948	0.94[AFR][1000 genomes]
rs1152900	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1161088	0.94[AFR][1000 genomes]
rs1177317	0.80[AFR][1000 genomes]
rs1252404	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252406	0.85[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252408	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252410	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252414	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1252418	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1252423	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1272090	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1621634	0.84[AFR][1000 genomes]
rs1658780	0.90[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1985475	0.90[CEU][hapmap]
rs710622	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs710623	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs710624	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs710798	0.85[AFR][1000 genomes]
rs710801	0.94[AFR][1000 genomes]
rs775307	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775308	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775310	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775624	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775628	0.85[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775634	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs775646	0.94[AFR][1000 genomes]
rs775647	0.94[AFR][1000 genomes]
rs775648	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775650	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs775653	0.94[AFR][1000 genomes]
rs775654	0.94[AFR][1000 genomes]
rs775656	0.89[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs775657	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs775661	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs775662	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs796508	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs796521	0.85[YRI][hapmap]
rs800166	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs800167	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs812325	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs812326	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs983630	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv525023	chr12:67672870-67708669	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv756	chr12:67703587-67744743	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1143758	CAND1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67681000-67714200	Weak transcription	Spleen	Spleen
2	chr12:67682200-67709000	Strong transcription	Dnd41	blood
3	chr12:67682200-67715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:67682600-67710600	Weak transcription	Right Ventricle	heart
5	chr12:67683400-67710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:67686000-67717000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:67686200-67708800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:67686200-67711200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:67686200-67716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:67686400-67708800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:67686400-67708800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr12:67686400-67708800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr12:67686400-67709000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:67686400-67709000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:67686400-67716000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:67686600-67708600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:67686600-67708800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:67686600-67708800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:67686800-67709000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:67687200-67708600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:67687600-67708600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:67687600-67708800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:67687600-67708800	Strong transcription	Liver	Liver
24	chr12:67687600-67708800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr12:67687800-67715400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:67688000-67709000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:67688200-67711400	Strong transcription	Placenta	Placenta
28	chr12:67688200-67717000	Strong transcription	NH-A	brain
29	chr12:67688400-67716000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:67688800-67711800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:67690000-67708800	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr12:67691000-67709400	Strong transcription	HSMM	muscle
33	chr12:67691000-67716000	Weak transcription	Fetal Intestine Small	intestine
34	chr12:67692200-67709200	Strong transcription	A549	lung
35	chr12:67695400-67708600	Strong transcription	Osteobl	bone
36	chr12:67695400-67709000	Strong transcription	HMEC	breast
37	chr12:67695600-67708800	Strong transcription	HUVEC	blood vessel
38	chr12:67696000-67708800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:67696000-67708800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:67696000-67708800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:67696000-67708800	Strong transcription	Adipose Nuclei	Adipose
42	chr12:67696000-67709000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:67696000-67709200	Strong transcription	Fetal Intestine Large	intestine
44	chr12:67696200-67709000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:67698400-67708800	Strong transcription	Primary B cells from cord blood	blood
46	chr12:67698400-67708800	Strong transcription	HSMMtube	muscle
47	chr12:67698600-67714000	Strong transcription	Fetal Thymus	thymus
48	chr12:67698800-67708800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr12:67698800-67709200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:67699000-67708800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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