Variant report

Variant	rs34077739
Chromosome Location	chr3:42591403-42591404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42589409..42591800-chr3:42596445..42599442,2	K562	blood:
2	chr3:42588925..42591573-chr3:42621859..42623455,2	K562	blood:
3	chr3:42588703..42591647-chr3:42620630..42623474,3	K562	blood:
4	chr3:42590321..42592623-chr3:42611370..42613403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13064597	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085143	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086680	0.89[EUR][1000 genomes]
rs13100261	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290976	0.90[EUR][1000 genomes]
rs339708	0.89[EUR][1000 genomes]
rs34196076	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243788	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34721465	0.87[EUR][1000 genomes]
rs35216140	1.00[ASN][1000 genomes]
rs35384559	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35871059	1.00[ASN][1000 genomes]
rs36043081	1.00[ASN][1000 genomes]
rs3733059	0.90[EUR][1000 genomes]
rs3733061	0.89[EUR][1000 genomes]
rs3900780	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994846	1.00[ASN][1000 genomes]
rs56047094	1.00[ASN][1000 genomes]
rs58645732	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[ASN][1000 genomes]
rs60535002	1.00[ASN][1000 genomes]
rs66933062	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67174294	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67583158	1.00[ASN][1000 genomes]
rs6771105	1.00[ASN][1000 genomes]
rs67832425	1.00[ASN][1000 genomes]
rs6790204	0.80[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6797491	1.00[ASN][1000 genomes]
rs6797545	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004576	1.00[ASN][1000 genomes]
rs71323162	1.00[ASN][1000 genomes]
rs72864022	1.00[ASN][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	1.00[ASN][1000 genomes]
rs7614219	1.00[ASN][1000 genomes]
rs7616701	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623867	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34077739	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	chr3:42575200-42594400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42577400-42592800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:42577600-42592000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:42577800-42597600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:42578400-42593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:42578400-42593400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:42581800-42594400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:42582000-42593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:42582000-42593600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:42582000-42594400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:42582200-42594400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:42582800-42591600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:42582800-42592000	Weak transcription	Ovary	ovary
14	chr3:42586000-42593400	Weak transcription	NH-A	brain
15	chr3:42586200-42595000	Weak transcription	Fetal Brain Male	brain
16	chr3:42586400-42591800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:42586400-42593200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:42586400-42593800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:42586400-42594400	Weak transcription	NHEK	skin
20	chr3:42586600-42593400	Weak transcription	A549	lung
21	chr3:42586600-42593800	Weak transcription	Right Ventricle	heart
22	chr3:42587000-42594200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:42587000-42594200	Weak transcription	HSMMtube	muscle
24	chr3:42587000-42594400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:42587000-42602400	Weak transcription	Colonic Mucosa	Colon
26	chr3:42587200-42591600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:42587400-42591800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:42587400-42591800	Weak transcription	Fetal Lung	lung
29	chr3:42587400-42597000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:42587400-42597200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:42587400-42606800	Weak transcription	Small Intestine	intestine
32	chr3:42587600-42594400	Weak transcription	HepG2	liver
33	chr3:42587800-42597000	Strong transcription	Fetal Thymus	thymus
34	chr3:42587800-42597000	Strong transcription	Thymus	Thymus
35	chr3:42587800-42611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:42588000-42613000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:42588200-42591600	Weak transcription	Primary B cells from cord blood	blood
38	chr3:42588400-42591800	Weak transcription	Osteobl	bone
39	chr3:42588400-42593400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:42588400-42613000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:42589000-42593800	Weak transcription	K562	blood
43	chr3:42589000-42594200	Weak transcription	NHDF-Ad	bronchial
44	chr3:42589000-42594600	Weak transcription	HSMM	muscle
45	chr3:42589000-42611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:42589200-42591600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:42589200-42611000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:42589400-42592800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:42589400-42592800	Weak transcription	Placenta	Placenta
50	chr3:42589400-42593400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links