Variant report

Variant	rs9548921
Chromosome Location	chr13:40328132-40328133
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12584772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012153	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012154	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303351	0.90[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs4603426	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322803	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563751	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6650473	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7329513	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994943	0.83[JPT][hapmap]
rs9315726	0.80[CHD][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs9532423	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532435	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548882	0.88[GIH][hapmap];0.92[TSI][hapmap]
rs9548886	0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs9548887	0.84[TSI][hapmap]
rs9548899	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548904	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548923	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548925	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576878	0.88[GIH][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548921	COG6	cis	multi-tissue	Pritchard
rs9548921	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
2	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
4	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
6	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
8	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:40297800-40329800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr13:40302000-40328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr13:40304000-40328800	Weak transcription	Dnd41	blood
12	chr13:40304600-40340000	Weak transcription	Osteobl	bone
13	chr13:40307600-40329400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:40309200-40331400	Weak transcription	Stomach Mucosa	stomach
15	chr13:40309200-40334600	Weak transcription	HepG2	liver
16	chr13:40311400-40347200	Weak transcription	HSMM	muscle
17	chr13:40311600-40329400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:40311600-40331200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:40311600-40339800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:40311600-40340000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:40311800-40331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:40311800-40339800	Weak transcription	Brain Anterior Caudate	brain
23	chr13:40311800-40340000	Weak transcription	Ovary	ovary
24	chr13:40312000-40340000	Weak transcription	Brain Angular Gyrus	brain
25	chr13:40312200-40329000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:40312200-40329800	Weak transcription	Aorta	Aorta
27	chr13:40312200-40331800	Weak transcription	Left Ventricle	heart
28	chr13:40312200-40333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:40312200-40340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr13:40312200-40340000	Weak transcription	Pancreas	Pancrea
31	chr13:40312200-40340200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr13:40312400-40329400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr13:40312400-40329400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr13:40312400-40329800	Weak transcription	Fetal Stomach	stomach
36	chr13:40314600-40331400	Weak transcription	Primary B cells from cord blood	blood
37	chr13:40315000-40340200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr13:40315200-40330600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr13:40315400-40329000	Weak transcription	Fetal Kidney	kidney
40	chr13:40320600-40329400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr13:40323000-40329400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:40325000-40330000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:40325000-40330400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr13:40325200-40334400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr13:40325600-40329000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:40325800-40339800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:40326000-40328400	Weak transcription	Right Ventricle	heart
48	chr13:40326000-40329000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr13:40326200-40329000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr13:40326200-40329400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links