Variant report

Variant	rs12204992
Chromosome Location	chr6:33741724-33741725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33733565..33735382-chr6:33741109..33742921,2	K562	blood:
2	chr6:33736395..33737905-chr6:33740079..33742724,2	K562	blood:
3	chr6:33677854..33679623-chr6:33741154..33743087,2	MCF-7	breast:
4	chr6:33738877..33740467-chr6:33741508..33744175,2	K562	blood:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10456420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456421	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947418	0.86[AFR][1000 genomes]
rs11755257	0.86[AFR][1000 genomes]
rs11757612	0.86[AFR][1000 genomes]
rs11758330	0.86[AFR][1000 genomes]
rs12153877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189725	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12192035	0.94[EUR][1000 genomes]
rs12192087	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193658	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198383	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199132	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12200154	0.86[AFR][1000 genomes]
rs12204620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205398	0.87[AFR][1000 genomes]
rs12211490	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12211554	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12211565	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12215329	0.93[EUR][1000 genomes]
rs12660955	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12662447	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195171	0.86[AFR][1000 genomes]
rs13200063	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs13206228	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13207666	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13213889	0.97[EUR][1000 genomes]
rs2274459	1.00[EUR][1000 genomes]
rs2296749	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34139049	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34339105	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34460651	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34472165	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34778247	1.00[ASN][1000 genomes]
rs34869648	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs34884883	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35095444	0.91[ASN][1000 genomes]
rs35274562	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35328423	0.88[EUR][1000 genomes]
rs35366046	0.92[EUR][1000 genomes]
rs35445446	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646598	0.92[EUR][1000 genomes]
rs35721478	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35797388	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs35964955	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36122085	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3793080	0.97[EUR][1000 genomes]
rs3806107	0.97[EUR][1000 genomes]
rs3818532	1.00[ASN][1000 genomes]
rs66617522	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66670017	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs68168863	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6925337	0.94[EUR][1000 genomes]
rs71565393	0.86[AFR][1000 genomes]
rs72880510	0.91[ASN][1000 genomes]
rs729376	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs751095	1.00[EUR][1000 genomes]
rs755239	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs877187	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:33736800-33743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:33737800-33742600	Weak transcription	Hela-S3	cervix
4	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
5	chr6:33738800-33741800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:33738800-33741800	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr6:33739000-33746000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:33739600-33742000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:33739800-33741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:33739800-33741800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:33739800-33741800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:33739800-33741800	Genic enhancers	Brain Hippocampus Middle	brain
15	chr6:33739800-33741800	Genic enhancers	NHLF	lung
16	chr6:33739800-33742000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:33739800-33742000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:33739800-33742400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:33739800-33742600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
24	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:33740000-33741800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:33740000-33741800	Genic enhancers	NHEK	skin
28	chr6:33740000-33742400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:33740000-33746000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:33740000-33749000	Strong transcription	Brain Anterior Caudate	brain
31	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:33740000-33752800	Strong transcription	Dnd41	blood
35	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:33740000-33753000	Strong transcription	HepG2	liver
37	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:33740200-33741800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:33740200-33741800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:33740200-33741800	Genic enhancers	HMEC	breast
43	chr6:33740200-33742000	Genic enhancers	HUVEC	blood vessel
44	chr6:33740200-33742600	Weak transcription	Psoas Muscle	Psoas
45	chr6:33740200-33743600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr6:33740200-33743800	Strong transcription	Brain Substantia Nigra	brain
47	chr6:33740200-33744600	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr6:33740200-33745800	Strong transcription	Brain Germinal Matrix	brain
49	chr6:33740200-33746600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:33740200-33747800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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