Variant report

Variant	rs9532412
Chromosome Location	chr13:40231915-40231916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40229934..40232193-chr13:40232512..40234424,2	K562	blood:

Variant related genes	Relation type
ENSG00000133103	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs3812882	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3812883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3812884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3812885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3812886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3812887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3812888	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4142370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4278626	0.96[ASN][1000 genomes]
rs4312180	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4384490	0.93[ASN][1000 genomes]
rs4415900	0.96[ASN][1000 genomes]
rs4941936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4941937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4941938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4941939	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4941941	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4943686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4943687	0.96[ASN][1000 genomes]
rs4943691	0.93[ASN][1000 genomes]
rs6563732	0.88[ASN][1000 genomes]
rs67976778	0.95[ASN][1000 genomes]
rs7325068	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7325655	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7327779	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7332791	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7334651	0.91[JPT][hapmap]
rs7335799	0.90[ASN][1000 genomes]
rs7984113	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs7984958	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9315720	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9315725	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9532408	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9532410	0.94[ASN][1000 genomes]
rs9532411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9532413	0.95[ASN][1000 genomes]
rs9532414	0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs9532420	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9548857	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9548859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9548862	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9548863	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9548865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9548866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9548867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9548868	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9548869	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9548870	0.96[ASN][1000 genomes]
rs9548875	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.95[ASN][1000 genomes]
rs9548880	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9548893	0.91[ASN][1000 genomes]
rs9548894	0.92[ASN][1000 genomes]
rs9548896	0.90[ASN][1000 genomes]
rs9548901	0.81[JPT][hapmap]
rs9548930	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs9566471	0.90[ASN][1000 genomes]
rs9566472	0.90[ASN][1000 genomes]
rs9576874	0.94[ASN][1000 genomes]
rs9576875	0.94[ASN][1000 genomes]
rs9576881	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9576882	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9532412	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230600-40232000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr13:40230600-40234400	Weak transcription	Placenta	Placenta
3	chr13:40230600-40252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:40230600-40254600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:40230600-40254600	Weak transcription	Lung	lung
6	chr13:40230600-40254800	Weak transcription	Aorta	Aorta
7	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
8	chr13:40230800-40232000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:40230800-40232000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr13:40230800-40232200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr13:40230800-40232200	Enhancers	Colon Smooth Muscle	Colon
12	chr13:40230800-40232400	Weak transcription	Ovary	ovary
13	chr13:40230800-40233000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr13:40230800-40234200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr13:40230800-40235400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:40230800-40236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr13:40230800-40236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr13:40230800-40236200	Weak transcription	Fetal Intestine Small	intestine
19	chr13:40230800-40238800	Weak transcription	Fetal Kidney	kidney
20	chr13:40230800-40238800	Weak transcription	HSMM	muscle
21	chr13:40230800-40239400	Weak transcription	HSMMtube	muscle
22	chr13:40230800-40239600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr13:40230800-40239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:40230800-40240000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:40230800-40246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
27	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
28	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
29	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
31	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
32	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
33	chr13:40231000-40232000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:40231000-40232000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr13:40231000-40232000	Enhancers	Brain Cingulate Gyrus	brain
36	chr13:40231000-40232200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:40231000-40232400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr13:40231000-40232800	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:40231000-40232800	Weak transcription	Fetal Brain Female	brain
40	chr13:40231000-40232800	Weak transcription	Fetal Intestine Large	intestine
41	chr13:40231000-40233000	Enhancers	Primary T cells from cord blood	blood
42	chr13:40231000-40233600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr13:40231000-40233600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr13:40231000-40233600	Weak transcription	NH-A	brain
45	chr13:40231000-40234000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:40231000-40234200	Weak transcription	Osteobl	bone
47	chr13:40231000-40234400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:40231000-40234400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr13:40231000-40234400	Weak transcription	Adipose Nuclei	Adipose
50	chr13:40231000-40234400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links