Variant report

Variant	rs7984958
Chromosome Location	chr13:40297032-40297033
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs3812882	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3812883	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3812884	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3812885	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3812886	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3812887	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3812888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4142370	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4245396	0.80[ASN][1000 genomes]
rs4278626	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4312180	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4384490	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4408422	0.83[ASN][1000 genomes]
rs4415900	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4941936	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4941937	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4941938	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4941939	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4941941	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4943686	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4943687	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4943691	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4943694	0.80[ASN][1000 genomes]
rs6563732	0.80[ASN][1000 genomes]
rs67976778	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7325068	0.83[ASN][1000 genomes]
rs7325655	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7327779	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7332791	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7335799	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984113	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9315720	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9315725	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9532408	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9532410	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9532411	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9532412	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9532413	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9532414	0.90[CEU][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9532420	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548857	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9548859	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9548862	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9548863	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9548865	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9548866	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9548867	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9548868	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs9548869	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9548870	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9548875	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548880	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548893	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548894	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548896	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548901	0.81[ASN][1000 genomes]
rs9566471	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566472	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576874	0.86[ASN][1000 genomes]
rs9576875	0.86[ASN][1000 genomes]
rs9576881	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9576882	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]

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
rs7984958	COG6	cis	Muscle Skeletal	GTEx
rs7984958	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
2	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
4	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
5	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
6	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:40263000-40297200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr13:40263200-40302600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:40267000-40297400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:40272000-40297400	Weak transcription	Ovary	ovary
12	chr13:40274000-40301600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr13:40282400-40310800	Weak transcription	Right Ventricle	heart
15	chr13:40283600-40310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:40283600-40311000	Weak transcription	Gastric	stomach
17	chr13:40284000-40298200	Weak transcription	Brain Anterior Caudate	brain
18	chr13:40284200-40310400	Weak transcription	Fetal Stomach	stomach
19	chr13:40284400-40302200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
21	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
22	chr13:40287000-40303000	Weak transcription	NHLF	lung
23	chr13:40287200-40297600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr13:40287400-40311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:40287400-40311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:40287400-40313000	Weak transcription	NHEK	skin
27	chr13:40287600-40310800	Weak transcription	HSMMtube	muscle
28	chr13:40289200-40297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:40289400-40297400	Weak transcription	Fetal Kidney	kidney
30	chr13:40290200-40311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:40290800-40299200	Strong transcription	Fetal Lung	lung
33	chr13:40291400-40298200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr13:40291400-40310800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:40291800-40297600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:40292000-40297200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:40292000-40298600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr13:40292000-40302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr13:40292000-40302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr13:40292000-40302800	Weak transcription	Fetal Intestine Small	intestine
41	chr13:40292000-40310400	Weak transcription	Fetal Brain Female	brain
42	chr13:40292000-40313400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr13:40292200-40297600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr13:40292200-40300200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr13:40292200-40311400	Weak transcription	Fetal Thymus	thymus
46	chr13:40292400-40297400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:40292400-40300400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:40292400-40300400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr13:40292400-40314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:40292600-40310600	Weak transcription	Fetal Muscle Trunk	muscle

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