Variant report

Variant	rs339725
Chromosome Location	chr3:42697605-42697606
allele	C/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	ZNF143	chr3:42697589-42697888	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOSL1	chr3:42697590-42698284	HCT-116	colon:	n/a	chr3:42697937-42697948 chr3:42697939-42697951 chr3:42698247-42698257 chr3:42697721-42697729 chr3:42697941-42697949
3	ZNF263	chr3:42697561-42697961	HEK293-T-REx	kidney:	n/a	chr3:42697693-42697702
4	CTBP2	chr3:42696182-42698042	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42695894..42698650-chr3:42786338..42788734,2	K562	blood:
2	chr3:42696300..42698185-chr3:42764015..42766530,4	K562	blood:
3	chr3:42629929..42632831-chr3:42695818..42698742,2	MCF-7	breast:
4	chr3:42696300..42697951-chr3:42764752..42766530,2	K562	blood:

Variant related genes	Relation type
ZBTB47	TF binding region
ENSG00000230084	TF binding region
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2136012	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271185	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271186	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2976533	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339658	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339723	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs339726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339727	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339728	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339733	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs342521	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342522	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342536	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342537	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774398	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4549	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs586082	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587712	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs597498	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs607568	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612733	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs614323	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs617722	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627664	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs638836	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639692	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs640689	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441892	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs663673	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689251	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704979	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8351	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs925457	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9865109	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs339725	NKTR	Cis_1M	lymphoblastoid	RTeQTL
rs339725	SEC22C	Cis_1M	lymphoblastoid	RTeQTL
rs339725	NKTR	cis	Nerve Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42696200-42698400	Enhancers	Fetal Brain Male	brain
2	chr3:42696400-42697800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:42696400-42698000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:42696600-42697800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:42696600-42697800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:42696600-42698000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:42696800-42697800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:42696800-42698000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:42696800-42698000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:42696800-42698000	Enhancers	Fetal Intestine Large	intestine
11	chr3:42696800-42698200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:42696800-42698400	Enhancers	Lung	lung
13	chr3:42696800-42698600	Enhancers	Spleen	Spleen
14	chr3:42696800-42701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:42697000-42697800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:42697000-42697800	Enhancers	Psoas Muscle	Psoas
17	chr3:42697000-42697800	Enhancers	HSMMtube	muscle
18	chr3:42697000-42698000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:42697000-42698200	Enhancers	Placenta	Placenta
20	chr3:42697000-42698400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:42697000-42698400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:42697000-42698400	Enhancers	Left Ventricle	heart
23	chr3:42697000-42698600	Enhancers	Stomach Mucosa	stomach
24	chr3:42697000-42699000	Enhancers	Esophagus	oesophagus
25	chr3:42697000-42699800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:42697000-42699800	Weak transcription	Aorta	Aorta
27	chr3:42697000-42700000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:42697000-42700600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr3:42697000-42702400	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr3:42697200-42697800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr3:42697200-42697800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:42697200-42698000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr3:42697200-42698000	Enhancers	Pancreas	Pancrea
34	chr3:42697200-42698200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:42697200-42698200	Enhancers	HUVEC	blood vessel
36	chr3:42697200-42698600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:42697200-42698600	Enhancers	NHDF-Ad	bronchial
38	chr3:42697200-42699000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:42697200-42699600	Weak transcription	Liver	Liver
40	chr3:42697200-42699800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr3:42697200-42701400	Genic enhancers	Fetal Muscle Leg	muscle
42	chr3:42697200-42703000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:42697200-42704600	Weak transcription	Primary B cells from cord blood	blood
44	chr3:42697400-42697800	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr3:42697400-42697800	Weak transcription	Fetal Intestine Small	intestine
46	chr3:42697400-42697800	Enhancers	Stomach Smooth Muscle	stomach
47	chr3:42697400-42698000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:42697400-42698000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:42697400-42698000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:42697400-42698000	Enhancers	Duodenum Smooth Muscle	Duodenum

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