Variant report

Variant	rs6771105
Chromosome Location	chr3:42651778-42651779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs13064597	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072295	0.82[EUR][1000 genomes]
rs13085143	1.00[ASN][1000 genomes]
rs13085695	0.82[EUR][1000 genomes]
rs13089845	0.82[EUR][1000 genomes]
rs13090902	0.82[EUR][1000 genomes]
rs13093680	0.82[EUR][1000 genomes]
rs13095447	0.82[EUR][1000 genomes]
rs13100261	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.97[EUR][1000 genomes]
rs17074662	0.82[EUR][1000 genomes]
rs17074673	0.82[EUR][1000 genomes]
rs17074674	0.82[EUR][1000 genomes]
rs17074693	0.82[EUR][1000 genomes]
rs2284303	0.82[EUR][1000 genomes]
rs2284304	0.82[EUR][1000 genomes]
rs2300057	0.82[EUR][1000 genomes]
rs2300058	0.82[EUR][1000 genomes]
rs2302352	0.82[EUR][1000 genomes]
rs33969824	0.82[EUR][1000 genomes]
rs339705	0.89[EUR][1000 genomes]
rs33984028	0.82[EUR][1000 genomes]
rs34077739	1.00[ASN][1000 genomes]
rs34196076	1.00[ASN][1000 genomes]
rs34243788	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683820	0.82[EUR][1000 genomes]
rs34687113	0.80[EUR][1000 genomes]
rs34762478	0.82[EUR][1000 genomes]
rs34801786	0.82[EUR][1000 genomes]
rs34852409	0.82[EUR][1000 genomes]
rs34977988	0.82[EUR][1000 genomes]
rs35216140	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676838	0.82[EUR][1000 genomes]
rs35871059	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35890296	0.82[EUR][1000 genomes]
rs36033201	0.82[EUR][1000 genomes]
rs36043081	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774401	0.82[EUR][1000 genomes]
rs3774402	0.82[EUR][1000 genomes]
rs3774404	0.82[EUR][1000 genomes]
rs3774407	0.82[EUR][1000 genomes]
rs3846058	0.82[EUR][1000 genomes]
rs3846059	0.82[EUR][1000 genomes]
rs3856737	0.82[EUR][1000 genomes]
rs3900780	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[ASN][1000 genomes]
rs55994846	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56797870	0.82[EUR][1000 genomes]
rs57259216	0.82[EUR][1000 genomes]
rs58645732	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.82[EUR][1000 genomes]
rs59914338	0.82[EUR][1000 genomes]
rs60232916	0.82[EUR][1000 genomes]
rs60348477	0.82[EUR][1000 genomes]
rs60535002	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61149998	0.82[EUR][1000 genomes]
rs6441928	0.82[EUR][1000 genomes]
rs66786953	0.81[EUR][1000 genomes]
rs66933062	1.00[ASN][1000 genomes]
rs67059259	0.82[EUR][1000 genomes]
rs67174294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.80[EUR][1000 genomes]
rs67583158	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778982	0.82[EUR][1000 genomes]
rs6782164	0.82[EUR][1000 genomes]
rs67832425	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788548	0.82[EUR][1000 genomes]
rs6790204	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6793186	0.82[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6795296	0.82[EUR][1000 genomes]
rs6797491	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028490	0.82[EUR][1000 genomes]
rs68071013	0.82[EUR][1000 genomes]
rs71323162	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864022	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864072	0.82[EUR][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616701	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617403	0.82[EUR][1000 genomes]
rs7617736	0.82[EUR][1000 genomes]
rs7623867	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7624628	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6771105	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643200-42672800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
3	chr3:42643800-42671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:42644000-42660000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:42644000-42671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:42644000-42671200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42644000-42671400	Weak transcription	HSMMtube	muscle
8	chr3:42644000-42672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:42644200-42655200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:42644200-42663200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:42644200-42672400	Weak transcription	Fetal Kidney	kidney
12	chr3:42644400-42653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:42644800-42660000	Weak transcription	Colonic Mucosa	Colon
14	chr3:42644800-42660200	Weak transcription	NH-A	brain
15	chr3:42645200-42652200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:42645200-42660200	Weak transcription	HMEC	breast
17	chr3:42645600-42653400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:42646000-42672000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:42646200-42651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:42646200-42654000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr3:42647000-42671400	Weak transcription	NHEK	skin
22	chr3:42647200-42668600	Weak transcription	Brain Germinal Matrix	brain
23	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:42647400-42654600	Weak transcription	Right Ventricle	heart
25	chr3:42647400-42672000	Weak transcription	NHLF	lung
26	chr3:42647600-42652600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:42647600-42654600	Weak transcription	A549	lung
28	chr3:42647600-42672000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:42647600-42677600	Weak transcription	Gastric	stomach
30	chr3:42647800-42652200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:42648000-42651800	Strong transcription	Fetal Intestine Large	intestine
32	chr3:42648000-42653600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:42648200-42651800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:42648200-42655400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:42648800-42672600	Weak transcription	Fetal Brain Female	brain
36	chr3:42649000-42657600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:42649200-42653600	Strong transcription	Fetal Intestine Small	intestine
38	chr3:42649400-42657000	Weak transcription	Primary B cells from cord blood	blood
39	chr3:42649600-42652600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:42649800-42652600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:42649800-42652800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:42649800-42653000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr3:42649800-42654400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:42649800-42671200	Weak transcription	Fetal Brain Male	brain
45	chr3:42650000-42651800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:42650000-42653600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:42650200-42653400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:42650200-42653600	Strong transcription	Dnd41	blood
49	chr3:42650200-42660000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:42650400-42651800	Strong transcription	Fetal Stomach	stomach

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