Variant report

Variant	rs339721
Chromosome Location	chr3:42702189-42702190
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42702080..42703037-chr3:42791145..42791706,3	K562	blood:
2	chr3:42702105..42703087-chr3:42796854..42797465,3	MCF-7	breast:
3	chr3:42700054..42702957-chr3:42774515..42776215,2	K562	blood:
4	chr3:42702115..42702691-chr3:42791094..42791699,3	MCF-7	breast:
5	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:
6	chr3:42695218..42698513-chr3:42700428..42704457,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	Chromatin interaction
ENSG00000244607	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114857	Chromatin interaction

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

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

rs_ID	r²[population]
rs13064311	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs13066173	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs13066333	0.81[ASN][1000 genomes]
rs168138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2068278	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs2271181	0.81[ASN][1000 genomes]
rs2271184	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs2271187	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs2284305	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs237064	0.81[ASN][1000 genomes]
rs2940407	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs3095258	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs339656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339720	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs339729	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342523	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap]
rs342534	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs342538	0.81[ASN][1000 genomes]
rs383937	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3888651	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs398743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60994254	0.94[ASN][1000 genomes]
rs612362	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs637852	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs638904	0.94[ASN][1000 genomes]
rs651180	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs654761	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs663258	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs664813	0.84[ASN][1000 genomes]
rs665206	0.88[ASN][1000 genomes]
rs704982	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs807863	0.88[ASN][1000 genomes]
rs82755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9311323	0.86[ASN][1000 genomes]
rs9311324	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs9813479	0.91[ASN][1000 genomes]
rs9819563	0.92[ASN][1000 genomes]
rs9828279	0.92[ASN][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	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	esv1818302	chr3:42688867-42709062	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv876731	chr3:42690285-42711655	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription 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	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs339721	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42697000-42702400	Genic enhancers	Fetal Muscle Trunk	muscle
2	chr3:42697200-42703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
4	chr3:42697400-42703000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:42697400-42706800	Weak transcription	HMEC	breast
6	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
8	chr3:42697600-42703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:42697600-42704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:42697600-42704800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:42697600-42707000	Weak transcription	A549	lung
12	chr3:42697600-42708000	Weak transcription	Colonic Mucosa	Colon
13	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:42697800-42702200	Weak transcription	HSMMtube	muscle
15	chr3:42697800-42702600	Genic enhancers	Brain Hippocampus Middle	brain
16	chr3:42697800-42707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:42697800-42707600	Strong transcription	Fetal Intestine Small	intestine
18	chr3:42697800-42707800	Weak transcription	Psoas Muscle	Psoas
19	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:42698000-42706400	Strong transcription	Fetal Stomach	stomach
21	chr3:42698200-42706600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:42698200-42708000	Weak transcription	HSMM	muscle
23	chr3:42698200-42708400	Weak transcription	HUVEC	blood vessel
24	chr3:42698400-42703800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:42698400-42704000	Genic enhancers	Right Ventricle	heart
26	chr3:42698600-42703200	Genic enhancers	Stomach Smooth Muscle	stomach
27	chr3:42698800-42703400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:42699200-42702400	Strong transcription	Fetal Intestine Large	intestine
29	chr3:42699200-42702600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:42699400-42703200	Enhancers	Fetal Heart	heart
31	chr3:42699400-42703400	Strong transcription	NHEK	skin
32	chr3:42699600-42702200	Genic enhancers	Brain Cingulate Gyrus	brain
33	chr3:42699800-42702600	Genic enhancers	Brain Anterior Caudate	brain
34	chr3:42699800-42703800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:42699800-42704800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:42699800-42705000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:42699800-42705600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
38	chr3:42699800-42706800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr3:42700000-42702600	Genic enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:42700000-42707000	Weak transcription	HepG2	liver
41	chr3:42700200-42702200	Genic enhancers	Gastric	stomach
42	chr3:42700200-42702600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:42700200-42702600	Genic enhancers	Brain Substantia Nigra	brain
44	chr3:42700200-42704600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:42700200-42705800	Strong transcription	Lung	lung
46	chr3:42700400-42702600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:42700400-42703800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:42700400-42705000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:42700800-42702400	Weak transcription	Liver	Liver
50	chr3:42700800-42705600	Weak transcription	Ovary	ovary

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