Variant report

Variant	rs6808052
Chromosome Location	chr3:46916051-46916052
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	BHLHE40	chr3:46916049-46916314	GM12878	blood:	n/a	n/a
2	MAX	chr3:46916006-46916310	K562	blood:	n/a	chr3:46916017-46916027 chr3:46916173-46916180 chr3:46916172-46916183 chr3:46916218-46916228 chr3:46916175-46916191
3	E2F6	chr3:46915974-46916476	H1-hESC	embryonic stem cell:	n/a	chr3:46916278-46916285 chr3:46916278-46916285 chr3:46916278-46916285
4	RUNX3	chr3:46915894-46916158	GM12878	blood:	n/a	n/a
5	MAX	chr3:46915978-46916363	K562	blood:	n/a	chr3:46916017-46916027 chr3:46916173-46916180 chr3:46916172-46916183 chr3:46916218-46916228 chr3:46916175-46916191
6	MAX	chr3:46915958-46916330	GM12878	blood:	n/a	chr3:46916017-46916027 chr3:46916173-46916180 chr3:46916172-46916183 chr3:46916218-46916228 chr3:46916175-46916191
7	RUNX3	chr3:46915941-46916209	GM12878	blood:	n/a	n/a
8	E2F6	chr3:46915997-46916300	K562	blood:	n/a	chr3:46916278-46916285 chr3:46916278-46916285 chr3:46916278-46916285

No.	Distal block	Cell Line	Cell type
1	chr3:46915275..46917060-chr3:46923765..46925773,2	K562	blood:
2	chr3:46908049..46912169-chr3:46912978..46916098,5	K562	blood:
3	chr3:46783774..46785518-chr3:46915413..46918248,2	MCF-7	breast:

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

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

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10461017	1.00[EUR][1000 genomes]
rs10461019	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11713537	1.00[MEX][hapmap];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[TSI][hapmap];1.00[EUR][1000 genomes]
rs1466273	1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1473384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473385	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1563431	1.00[EUR][1000 genomes]
rs1563432	1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs2124509	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	1.00[MEX][hapmap];1.00[TSI][hapmap];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[MEX][hapmap];1.00[TSI][hapmap];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	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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[EUR][1000 genomes]
rs4682847	1.00[TSI][hapmap];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]
rs4683282	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4683283	1.00[ASW][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683284	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683291	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683292	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4683293	1.00[EUR][1000 genomes]
rs4683303	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442014	1.00[EUR][1000 genomes]
rs6442015	1.00[EUR][1000 genomes]
rs6442041	0.83[YRI][hapmap];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[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6809904	1.00[EUR][1000 genomes]
rs7621530	1.00[EUR][1000 genomes]
rs7624549	1.00[EUR][1000 genomes]
rs7630904	1.00[EUR][1000 genomes]
rs7638549	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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[MEX][hapmap];1.00[TSI][hapmap];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[TSI][hapmap];1.00[EUR][1000 genomes]
rs936182	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs936185	1.00[TSI][hapmap];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	0.89[AMR][1000 genomes];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[TSI][hapmap];1.00[EUR][1000 genomes]
rs9836801	1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs9850151	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];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:14 , 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	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv590207	chr3:46903361-46919379	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46906800-46920000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:46909600-46917000	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:46910000-46916400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:46910000-46916400	Weak transcription	Psoas Muscle	Psoas
5	chr3:46910000-46916800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:46910200-46916800	Weak transcription	Esophagus	oesophagus
7	chr3:46910600-46916600	Enhancers	Right Atrium	heart
8	chr3:46910600-46918400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:46911000-46917200	Enhancers	Right Ventricle	heart
10	chr3:46912200-46916600	Enhancers	Placenta	Placenta
11	chr3:46912200-46921000	Enhancers	Fetal Heart	heart
12	chr3:46912400-46916600	Enhancers	Fetal Lung	lung
13	chr3:46912600-46916800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr3:46912600-46917000	Enhancers	Ovary	ovary
15	chr3:46912600-46918600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr3:46913000-46916200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr3:46913000-46916800	Enhancers	Lung	lung
18	chr3:46913200-46917400	Bivalent Enhancer	Fetal Stomach	stomach
19	chr3:46913400-46917000	Enhancers	Left Ventricle	heart
20	chr3:46913600-46916600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:46913600-46920200	Weak transcription	Pancreas	Pancrea
22	chr3:46914000-46916600	Enhancers	Aorta	Aorta
23	chr3:46914000-46917600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:46914000-46918000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:46914200-46916400	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:46914200-46917400	Enhancers	Fetal Thymus	thymus
27	chr3:46914200-46918000	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:46914400-46916200	Enhancers	Primary B cells from cord blood	blood
29	chr3:46914400-46917800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:46914400-46918200	Enhancers	Fetal Kidney	kidney
31	chr3:46914400-46921400	Enhancers	Fetal Intestine Large	intestine
32	chr3:46914600-46919600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:46914800-46917000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:46915000-46916200	Weak transcription	Spleen	Spleen
35	chr3:46915000-46916400	Enhancers	GM12878-XiMat	blood
36	chr3:46915000-46916600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:46915200-46916400	Enhancers	Colon Smooth Muscle	Colon
38	chr3:46915400-46916600	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:46915400-46917400	Enhancers	Stomach Smooth Muscle	stomach
40	chr3:46915400-46917800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:46915400-46917800	Weak transcription	HSMM	muscle
42	chr3:46915400-46921600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:46915600-46916200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:46915600-46916200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr3:46915600-46916200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:46915600-46916400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:46915600-46916600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:46915600-46916600	Enhancers	Thymus	Thymus
49	chr3:46915800-46916200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:46915800-46916400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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