Variant report

Variant	rs2791458
Chromosome Location	chr6:5455161-5455162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5455034..5457596-chr6:5459159..5460952,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12192898	0.89[EUR][1000 genomes]
rs1364555	0.90[JPT][hapmap]
rs17133279	0.90[JPT][hapmap]
rs17140384	0.90[JPT][hapmap]
rs17140394	0.90[JPT][hapmap]
rs183221	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183222	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200194	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200195	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200196	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200197	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200199	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200202	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2432780	0.90[JPT][hapmap]
rs2432785	0.90[JPT][hapmap]
rs2432786	0.90[JPT][hapmap]
rs2432788	0.88[JPT][hapmap]
rs2503818	0.90[JPT][hapmap]
rs2503823	0.90[JPT][hapmap]
rs2503835	0.90[JPT][hapmap]
rs2552289	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003869	0.90[JPT][hapmap]
rs554425	0.90[ASN][1000 genomes]
rs656078	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72817717	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760235	0.90[JPT][hapmap]
rs9502295	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1030744	chr6:5328012-5458222	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv600885	chr6:5424762-5455161	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2791458	GMDS	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5421600-5455400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:5421600-5457400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:5433600-5457400	Weak transcription	Left Ventricle	heart
4	chr6:5433600-5461400	Weak transcription	Fetal Stomach	stomach
5	chr6:5434200-5487000	Weak transcription	Aorta	Aorta
6	chr6:5437400-5471200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:5438200-5471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:5439600-5459800	Weak transcription	Primary T cells from cord blood	blood
9	chr6:5443000-5457200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:5443800-5458200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:5444000-5456600	Weak transcription	Lung	lung
12	chr6:5444000-5456800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:5444000-5457000	Weak transcription	Esophagus	oesophagus
14	chr6:5444000-5457000	Weak transcription	Pancreas	Pancrea
15	chr6:5444400-5457000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:5444400-5458200	Weak transcription	Psoas Muscle	Psoas
17	chr6:5447600-5460600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:5448200-5456400	Weak transcription	NHEK	skin
19	chr6:5448200-5457400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:5448600-5466800	Weak transcription	Primary B cells from cord blood	blood
21	chr6:5449000-5499400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:5450600-5457000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:5450800-5457200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:5450800-5459600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:5451200-5457000	Weak transcription	Gastric	stomach
26	chr6:5453000-5471000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:5453200-5460600	Weak transcription	Dnd41	blood
28	chr6:5453400-5455200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:5453800-5457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:5453800-5457000	Weak transcription	Brain Substantia Nigra	brain
31	chr6:5454200-5457400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:5454200-5458400	Weak transcription	Colonic Mucosa	Colon
33	chr6:5454800-5455400	Strong transcription	Liver	Liver
34	chr6:5454800-5472000	Weak transcription	Spleen	Spleen
35	chr6:5455000-5455200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:5455000-5455200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:5455000-5455200	Enhancers	Brain Angular Gyrus	brain
38	chr6:5455000-5455200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:5455000-5455200	Active TSS	Fetal Brain Female	brain
40	chr6:5455000-5455200	Enhancers	Right Atrium	heart
41	chr6:5455000-5455200	Enhancers	Right Ventricle	heart
42	chr6:5455000-5455400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:5455000-5455400	Flanking Active TSS	Fetal Lung	lung
44	chr6:5455000-5459000	Enhancers	Adipose Nuclei	Adipose
45	chr6:5455000-5460000	Enhancers	Fetal Brain Male	brain

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