Variant report

Variant	rs339724
Chromosome Location	chr3:42700456-42700457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr3:42700432-42701333	K562	blood:	n/a	chr3:42700704-42700725
2	ZNF263	chr3:42700448-42702000	HEK293-T-REx	kidney:	n/a	chr3:42700704-42700725 chr3:42701783-42701792

No.	Distal block	Cell Line	Cell type
1	chr3:42693324..42695216-chr3:42700072..42702167,2	MCF-7	breast:
2	chr3:42700054..42702957-chr3:42774515..42776215,2	K562	blood:
3	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:
4	chr3:42695218..42698513-chr3:42700428..42704457,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230084	TF binding region
ENSG00000114857	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000244607	Chromatin interaction
ENSG00000230084	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13064311	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13066173	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs168138	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2068278	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs2271184	0.83[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs2271187	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2284305	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2940407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3095258	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs339656	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs339720	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs339721	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs339729	0.89[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs339735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs342523	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs342534	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs383937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3888651	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs398743	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60994254	0.90[ASN][1000 genomes]
rs612362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs637852	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs638904	0.90[ASN][1000 genomes]
rs651180	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs654761	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs663258	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs664813	0.81[ASN][1000 genomes]
rs665206	0.84[ASN][1000 genomes]
rs704982	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs807863	0.84[ASN][1000 genomes]
rs82755	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9311323	0.81[ASN][1000 genomes]
rs9311324	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9813479	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9819563	0.87[ASN][1000 genomes]
rs9828279	0.82[EUR][1000 genomes];0.87[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
rs339724	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42696800-42701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:42697000-42700600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:42697000-42702400	Genic enhancers	Fetal Muscle Trunk	muscle
4	chr3:42697200-42701400	Genic enhancers	Fetal Muscle Leg	muscle
5	chr3:42697200-42703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:42697400-42700800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:42697400-42701200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:42697400-42702000	Weak transcription	Fetal Kidney	kidney
10	chr3:42697400-42703000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:42697400-42706800	Weak transcription	HMEC	breast
12	chr3:42697400-42708800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:42697400-42708800	Weak transcription	Fetal Lung	lung
14	chr3:42697600-42703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:42697600-42704600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:42697600-42704800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:42697600-42707000	Weak transcription	A549	lung
18	chr3:42697600-42708000	Weak transcription	Colonic Mucosa	Colon
19	chr3:42697600-42709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:42697800-42701000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:42697800-42702200	Weak transcription	HSMMtube	muscle
22	chr3:42697800-42702600	Genic enhancers	Brain Hippocampus Middle	brain
23	chr3:42697800-42707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:42697800-42707600	Strong transcription	Fetal Intestine Small	intestine
25	chr3:42697800-42707800	Weak transcription	Psoas Muscle	Psoas
26	chr3:42697800-42709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:42698000-42701200	Weak transcription	NH-A	brain
28	chr3:42698000-42706400	Strong transcription	Fetal Stomach	stomach
29	chr3:42698200-42701200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:42698200-42701200	Weak transcription	Osteobl	bone
31	chr3:42698200-42706600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:42698200-42708000	Weak transcription	HSMM	muscle
33	chr3:42698200-42708400	Weak transcription	HUVEC	blood vessel
34	chr3:42698400-42701200	Strong transcription	NHLF	lung
35	chr3:42698400-42703800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:42698400-42704000	Genic enhancers	Right Ventricle	heart
37	chr3:42698600-42701200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:42698600-42701200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:42698600-42701400	Weak transcription	NHDF-Ad	bronchial
40	chr3:42698600-42703200	Genic enhancers	Stomach Smooth Muscle	stomach
41	chr3:42698800-42703400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:42699000-42700600	Genic enhancers	Esophagus	oesophagus
43	chr3:42699000-42701600	Strong transcription	Fetal Brain Female	brain
44	chr3:42699200-42702400	Strong transcription	Fetal Intestine Large	intestine
45	chr3:42699200-42702600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:42699400-42701000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:42699400-42701200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:42699400-42701200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:42699400-42701600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:42699400-42702000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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