Variant report

Variant	rs17694832
Chromosome Location	chr14:39860026-39860027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10137623	0.80[CHB][hapmap]
rs1056345	0.92[CEU][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11560068	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12879584	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12881098	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12884137	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12885079	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12886403	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12891299	0.80[AMR][1000 genomes]
rs17621388	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17696574	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955704	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2148507	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2415542	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2415546	0.89[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34173090	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34629111	0.83[AMR][1000 genomes]
rs34651350	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34654496	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34697019	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34829840	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34983854	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35026953	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35297616	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35690918	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36090203	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4531652	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56127968	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7143942	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap]
rs7152028	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72675474	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72677625	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8006182	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs8014839	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs8015094	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs8017737	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8020472	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8020596	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17694832	SEC23A	cis	parietal	SCAN
rs17694832	TRAPPC6B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
2	chr14:39818800-39867200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr14:39835400-39872400	Weak transcription	Fetal Muscle Leg	muscle
4	chr14:39836200-39872800	Weak transcription	Esophagus	oesophagus
5	chr14:39836400-39870600	Weak transcription	Gastric	stomach
6	chr14:39840000-39863200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr14:39840000-39863400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr14:39840000-39864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:39840000-39867000	Weak transcription	Left Ventricle	heart
10	chr14:39840000-39867400	Weak transcription	Pancreas	Pancrea
11	chr14:39840000-39882600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:39840200-39867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr14:39840600-39864400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr14:39841000-39865800	Weak transcription	Primary B cells from cord blood	blood
15	chr14:39841200-39867000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:39841400-39862800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr14:39846200-39864800	Weak transcription	NHEK	skin
18	chr14:39846200-39878800	Weak transcription	Right Ventricle	heart
19	chr14:39846400-39862400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:39846400-39864600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:39846400-39867200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr14:39846600-39862600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr14:39846600-39864600	Weak transcription	HepG2	liver
24	chr14:39846600-39864600	Weak transcription	NH-A	brain
25	chr14:39846600-39864800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:39846600-39866600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:39846800-39862600	Weak transcription	Adipose Nuclei	Adipose
28	chr14:39846800-39872400	Weak transcription	HSMMtube	muscle
29	chr14:39848000-39862600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:39850400-39870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr14:39851000-39866800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:39851200-39866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:39851200-39868600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:39851400-39868600	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:39851400-39868600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr14:39851600-39862400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:39851800-39864600	Weak transcription	Fetal Intestine Large	intestine
38	chr14:39852800-39863400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr14:39852800-39864600	Weak transcription	Dnd41	blood
40	chr14:39853000-39867400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:39853000-39867400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:39853200-39866200	Weak transcription	GM12878-XiMat	blood
43	chr14:39853200-39867800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr14:39853600-39862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr14:39853600-39866200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr14:39853600-39867200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr14:39853600-39874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr14:39853800-39863600	Weak transcription	Primary T cells from cord blood	blood
49	chr14:39854400-39872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr14:39855200-39863400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links