Variant report

Variant	rs4683301
Chromosome Location	chr3:46931478-46931479
allele	A/T
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	RCOR1	chr3:46930883-46931531	K562	blood:	n/a	n/a
2	STAT5A	chr3:46931463-46931897	K562	blood:	n/a	n/a
3	NFIC	chr3:46931073-46931742	ECC-1	luminal epithelium:	n/a	chr3:46931376-46931393 chr3:46931377-46931393
4	NFIC	chr3:46931119-46931662	ECC-1	luminal epithelium:	n/a	chr3:46931376-46931393 chr3:46931377-46931393
5	ZNF263	chr3:46930942-46931943	HEK293-T-REx	kidney:	n/a	n/a
6	ELF1	chr3:46931187-46931564	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46923987..46927246-chr3:46931255..46933897,4	K562	blood:
2	chr3:46929621..46931545-chr3:47041151..47042840,2	K562	blood:
3	chr3:46929163..46931629-chr3:46932279..46935009,2	K562	blood:

Variant related genes	Relation type
PTH1R	TF binding region
ENSG00000268537	TF binding region
ENSG00000160796	Chromatin interaction
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1001284	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1079276	0.81[YRI][hapmap]
rs10865943	0.88[ASN][1000 genomes]
rs11130110	0.81[YRI][hapmap]
rs11130111	0.81[YRI][hapmap]
rs1138518	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11705936	0.88[ASN][1000 genomes]
rs11719795	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs1466275	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2168443	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2242116	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290545	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2290546	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2305634	0.81[YRI][hapmap]
rs4539969	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4587	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4682837	0.81[YRI][hapmap]
rs4682845	0.89[ASN][1000 genomes]
rs4683296	0.91[CHB][hapmap];0.90[ASN][1000 genomes]
rs4683297	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4683298	0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs4683299	0.86[ASN][1000 genomes]
rs4683300	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442038	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs6442039	0.81[ASN][1000 genomes]
rs6442040	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6780601	0.90[ASN][1000 genomes]
rs724448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs724449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.85[CHD][hapmap];0.94[ASN][1000 genomes]
rs7623898	0.90[ASN][1000 genomes]
rs7628747	0.81[YRI][hapmap]
rs7635480	0.81[ASN][1000 genomes]
rs7645278	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7646906	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9852082	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs9855938	0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4683301	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs4683301	CCDC12	cis	cerebellum	SCAN
rs4683301	IMPDH2	cis	parietal	SCAN
rs4683301	SCAP	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46925200-46933000	Weak transcription	Pancreas	Pancrea
2	chr3:46925800-46933000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:46926000-46933400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:46926600-46933000	Weak transcription	Left Ventricle	heart
5	chr3:46926600-46933200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:46926600-46933400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:46929000-46931800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
8	chr3:46929400-46933000	Enhancers	Fetal Lung	lung
9	chr3:46930000-46931800	Enhancers	Right Atrium	heart
10	chr3:46930200-46931600	Enhancers	Adipose Nuclei	Adipose
11	chr3:46930200-46931800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:46930400-46931800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr3:46930400-46932000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr3:46930400-46932000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr3:46930400-46932000	Enhancers	Lung	lung
16	chr3:46930400-46932200	Enhancers	Right Ventricle	heart
17	chr3:46930400-46933600	Enhancers	Ovary	ovary
18	chr3:46930400-46933800	Enhancers	Spleen	Spleen
19	chr3:46930600-46931600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:46930600-46932000	Enhancers	Stomach Smooth Muscle	stomach
21	chr3:46930600-46933800	Bivalent Enhancer	Placenta	Placenta
22	chr3:46930800-46931600	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr3:46930800-46931800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr3:46930800-46932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:46930800-46933000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:46931000-46931800	Enhancers	Fetal Heart	heart
27	chr3:46931000-46932000	Enhancers	Fetal Intestine Large	intestine
28	chr3:46931000-46933200	Enhancers	Fetal Kidney	kidney
29	chr3:46931200-46931600	Enhancers	HSMMtube	muscle
30	chr3:46931200-46931800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:46931200-46931800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:46931200-46931800	Bivalent Enhancer	Fetal Intestine Small	intestine
33	chr3:46931200-46931800	Bivalent Enhancer	Fetal Thymus	thymus
34	chr3:46931200-46932000	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:46931200-46932000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:46931200-46932000	Bivalent Enhancer	Fetal Stomach	stomach
37	chr3:46931200-46932000	Enhancers	K562	blood
38	chr3:46931200-46932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:46931200-46933400	Weak transcription	Brain Substantia Nigra	brain
40	chr3:46931400-46931600	Bivalent Enhancer	Brain Germinal Matrix	brain
41	chr3:46931400-46931600	Enhancers	Colon Smooth Muscle	Colon
42	chr3:46931400-46932800	Weak transcription	Esophagus	oesophagus
43	chr3:46931400-46933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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