Variant report

Variant	rs17281703
Chromosome Location	chr3:119243549-119243550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119187617..119189310-chr3:119243541..119246268,2	MCF-7	breast:
2	chr3:119237156..119239321-chr3:119242706..119244832,2	K562	blood:
3	chr3:119243377..119244472-chr3:119399849..119400744,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163389	Chromatin interaction
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1132202	1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs11556604	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631504	1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12639070	0.82[EUR][1000 genomes]
rs13084583	1.00[YRI][hapmap]
rs16829809	0.84[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs17281612	1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs17281647	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2282173	0.83[EUR][1000 genomes]
rs2282175	1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs57509340	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs58968288	0.80[EUR][1000 genomes]
rs59551807	0.80[EUR][1000 genomes]
rs60588168	0.83[EUR][1000 genomes]
rs60671082	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs61740281	0.82[EUR][1000 genomes]
rs6772534	0.92[MEX][hapmap];0.85[TSI][hapmap]
rs6782411	0.84[JPT][hapmap];0.84[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17281703	SEC22A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
3	chr3:119220800-119243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:119221000-119244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:119221200-119243600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:119221200-119244400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
8	chr3:119221600-119244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119226000-119245200	Strong transcription	Liver	Liver
13	chr3:119226600-119245200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:119227400-119245400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:119228000-119243600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:119229200-119244600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:119230600-119245400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:119230800-119244400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:119231200-119244000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:119231800-119244000	Strong transcription	Adipose Nuclei	Adipose
22	chr3:119231800-119244800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:119231800-119245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood
25	chr3:119232000-119244200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:119232000-119244200	Strong transcription	Brain Substantia Nigra	brain
27	chr3:119232000-119245200	Strong transcription	A549	lung
28	chr3:119233000-119245200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:119233200-119243600	Strong transcription	Brain Anterior Caudate	brain
30	chr3:119233200-119244600	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr3:119234400-119244600	Strong transcription	Fetal Intestine Large	intestine
32	chr3:119234600-119244400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr3:119235800-119243600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:119237600-119245200	Strong transcription	Fetal Thymus	thymus
35	chr3:119237800-119244800	Weak transcription	Hela-S3	cervix
36	chr3:119237800-119245000	Weak transcription	Colonic Mucosa	Colon
37	chr3:119237800-119245400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:119237800-119245800	Weak transcription	Small Intestine	intestine
39	chr3:119237800-119246000	Weak transcription	Right Ventricle	heart
40	chr3:119237800-119246400	Weak transcription	Pancreas	Pancrea
41	chr3:119237800-119246600	Weak transcription	Esophagus	oesophagus
42	chr3:119237800-119248000	Weak transcription	Aorta	Aorta
43	chr3:119237800-119251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:119237800-119255800	Weak transcription	Spleen	Spleen
45	chr3:119238000-119245000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:119238000-119245200	Strong transcription	Dnd41	blood
47	chr3:119238000-119245400	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:119238000-119248400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:119238200-119245200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:119238200-119245200	Strong transcription	Fetal Lung	lung

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