Variant report

Variant	rs2385863
Chromosome Location	chr3:46939186-46939187
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:46939184-46939663	MCF-7	breast:	n/a	n/a
2	RAD21	chr3:46939168-46939522	HepG2	liver:	n/a	n/a
3	CTCF	chr3:46939153-46939525	K562	blood:	n/a	n/a
4	RAD21	chr3:46939176-46939626	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr3:46939181-46939558	K562	blood:	n/a	n/a
6	CTCF	chr3:46939167-46939583	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:46939174-46939666	HCT-116	colon:	n/a	n/a
8	POLR2A	chr3:46938433-46940961	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46935290..46938710-chr3:46938764..46942918,5	K562	blood:
2	chr3:46929548..46935187-chr3:46936132..46940432,7	K562	blood:
3	chr3:46924894..46926955-chr3:46938452..46941314,2	K562	blood:
4	chr3:46933982..46936274-chr3:46938142..46940231,2	MCF-7	breast:
5	chr3:46920420..46922046-chr3:46938380..46939888,2	MCF-7	breast:

No data

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

Extended variants
information (count: 151 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10461017	1.00[EUR][1000 genomes]
rs10461019	1.00[EUR][1000 genomes]
rs11130108	1.00[EUR][1000 genomes]
rs11130109	1.00[EUR][1000 genomes]
rs11706212	1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11709876	1.00[EUR][1000 genomes]
rs11713537	1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	1.00[EUR][1000 genomes]
rs13062185	1.00[EUR][1000 genomes]
rs13079416	1.00[EUR][1000 genomes]
rs13082531	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	1.00[EUR][1000 genomes]
rs1463394	1.00[EUR][1000 genomes]
rs1466272	1.00[EUR][1000 genomes]
rs1466273	1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs2124509	1.00[EUR][1000 genomes]
rs2385868	1.00[EUR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs3930202	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	1.00[EUR][1000 genomes]
rs4289375	1.00[EUR][1000 genomes]
rs4324490	1.00[EUR][1000 genomes]
rs4373094	1.00[EUR][1000 genomes]
rs4378998	1.00[EUR][1000 genomes]
rs4389512	1.00[EUR][1000 genomes]
rs4450857	1.00[EUR][1000 genomes]
rs4478107	1.00[EUR][1000 genomes]
rs4519738	1.00[EUR][1000 genomes]
rs4522803	1.00[EUR][1000 genomes]
rs4525902	1.00[EUR][1000 genomes]
rs4543047	1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	1.00[EUR][1000 genomes]
rs4682833	1.00[EUR][1000 genomes]
rs4682834	1.00[EUR][1000 genomes]
rs4682835	1.00[EUR][1000 genomes]
rs4682836	1.00[EUR][1000 genomes]
rs4682838	1.00[EUR][1000 genomes]
rs4682841	1.00[EUR][1000 genomes]
rs4682843	1.00[EUR][1000 genomes]
rs4682846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683261	1.00[EUR][1000 genomes]
rs4683262	1.00[EUR][1000 genomes]
rs4683265	1.00[EUR][1000 genomes]
rs4683277	1.00[EUR][1000 genomes]
rs4683279	1.00[EUR][1000 genomes]
rs4683283	1.00[EUR][1000 genomes]
rs4683284	1.00[EUR][1000 genomes]
rs4683285	1.00[EUR][1000 genomes]
rs4683286	1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	1.00[EUR][1000 genomes]
rs4683290	1.00[EUR][1000 genomes]
rs4683291	1.00[EUR][1000 genomes]
rs4683292	1.00[EUR][1000 genomes]
rs4683293	1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442014	1.00[EUR][1000 genomes]
rs6442015	1.00[EUR][1000 genomes]
rs6442041	1.00[EUR][1000 genomes]
rs6442042	1.00[EUR][1000 genomes]
rs6442043	1.00[EUR][1000 genomes]
rs6442044	1.00[EUR][1000 genomes]
rs6442047	1.00[EUR][1000 genomes]
rs6442048	1.00[EUR][1000 genomes]
rs6766676	1.00[EUR][1000 genomes]
rs6768169	1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6785462	1.00[EUR][1000 genomes]
rs6804732	1.00[EUR][1000 genomes]
rs6806521	1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6809904	1.00[EUR][1000 genomes]
rs7621530	1.00[EUR][1000 genomes]
rs7624549	1.00[EUR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	1.00[EUR][1000 genomes]
rs7638549	1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643868	1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	1.00[EUR][1000 genomes]
rs7649941	1.00[EUR][1000 genomes]
rs7650142	1.00[EUR][1000 genomes]
rs7650245	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	1.00[EUR][1000 genomes]
rs936178	1.00[EUR][1000 genomes]
rs936179	1.00[EUR][1000 genomes]
rs936180	1.00[EUR][1000 genomes]
rs936181	1.00[EUR][1000 genomes]
rs936182	1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs939409	1.00[EUR][1000 genomes]
rs939410	1.00[EUR][1000 genomes]
rs939411	1.00[EUR][1000 genomes]
rs939412	1.00[EUR][1000 genomes]
rs939413	1.00[EUR][1000 genomes]
rs939415	1.00[EUR][1000 genomes]
rs939416	1.00[EUR][1000 genomes]
rs939417	1.00[EUR][1000 genomes]
rs939420	1.00[EUR][1000 genomes]
rs9810881	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9836801	1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][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	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
9	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
10	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
11	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
12	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46934400-46940000	Weak transcription	Pancreas	Pancrea
2	chr3:46934400-46951000	Weak transcription	Psoas Muscle	Psoas
3	chr3:46934600-46939600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:46934600-46939800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:46934600-46939800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:46934600-46939800	Weak transcription	Esophagus	oesophagus
7	chr3:46934600-46949400	Weak transcription	Fetal Kidney	kidney
8	chr3:46934800-46940000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:46934800-46940200	Weak transcription	HUVEC	blood vessel
10	chr3:46935000-46939400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:46935000-46940000	Weak transcription	Gastric	stomach
12	chr3:46935000-46940000	Weak transcription	Ovary	ovary
13	chr3:46935200-46939800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:46935200-46939800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:46935200-46939800	Weak transcription	HSMM	muscle
16	chr3:46935400-46939600	Weak transcription	HSMMtube	muscle
17	chr3:46935400-46940000	Weak transcription	Right Atrium	heart
18	chr3:46935400-46940400	Weak transcription	Left Ventricle	heart
19	chr3:46935600-46939800	Weak transcription	Lung	lung
20	chr3:46935800-46939400	Weak transcription	Spleen	Spleen
21	chr3:46935800-46939600	Weak transcription	Fetal Heart	heart
22	chr3:46936800-46939400	Weak transcription	Right Ventricle	heart
23	chr3:46936800-46939400	Weak transcription	K562	blood
24	chr3:46937000-46939600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:46937200-46939200	Weak transcription	Liver	Liver
26	chr3:46937600-46939400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:46937800-46939600	Weak transcription	Fetal Lung	lung
28	chr3:46938000-46940000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links