Variant report

Variant	rs12204396
Chromosome Location	chr6:15326456-15326457
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:15326389-15326622	HepG2	liver:	n/a	chr6:15326532-15326543
2	RELA	chr6:15325412-15326617	GM12878	blood:	n/a	n/a
3	CEBPB	chr6:15326386-15326688	Hela-S3	cervix:	n/a	chr6:15326532-15326543
4	RUNX3	chr6:15326310-15326752	GM12878	blood:	n/a	n/a
5	TBP	chr6:15325664-15326512	GM12878	blood:	n/a	n/a
6	CREB1	chr6:15326267-15326786	GM12878	blood:	n/a	n/a
7	CREB1	chr6:15326282-15326811	GM12878	blood:	n/a	n/a
8	ZNF384	chr6:15326356-15326557	GM12878	blood:	n/a	n/a
9	ATF2	chr6:15325639-15326745	GM12878	blood:	n/a	n/a
10	EP300	chr6:15325765-15326640	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:15326446-15326873	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:15326368-15326938	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:15326240-15326735	H1-hESC	embryonic stem cell:	n/a	n/a
14	EP300	chr6:15325894-15326482	GM12878	blood:	n/a	n/a
15	RUNX3	chr6:15325240-15326833	GM12878	blood:	n/a	n/a
16	RELA	chr6:15325653-15326617	GM18505	blood:	n/a	n/a
17	TCF12	chr6:15326406-15326690	GM12878	blood:	n/a	n/a
18	CEBPB	chr6:15326390-15326680	K562	blood:	n/a	chr6:15326532-15326543
19	EP300	chr6:15326348-15326629	GM12878	blood:	n/a	n/a
20	NFIC	chr6:15325688-15327050	GM12878	blood:	n/a	n/a
21	MTA3	chr6:15325374-15326812	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:15326389-15326887	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:15321161..15324088-chr6:15325760..15327373,2	K562	blood:
2	chr6:15320928..15323607-chr6:15325318..15329724,5	K562	blood:
3	chr6:15248004..15250330-chr6:15324617..15327935,3	K562	blood:
4	chr6:15245706..15248419-chr6:15325592..15327879,2	MCF-7	breast:
5	chr6:15325585..15327552-chr6:15333592..15336004,2	K562	blood:
6	chr6:15325527..15327943-chr6:15329707..15332701,2	K562	blood:
7	chr6:15247440..15249791-chr6:15324617..15327427,3	K562	blood:

No data

Variant related genes	Relation type
RNU6-645P	TF binding region
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12190529	1.00[AMR][1000 genomes]
rs12210722	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15311200-15330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:15313200-15326600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:15314200-15326600	Weak transcription	Ovary	ovary
4	chr6:15314400-15327600	Weak transcription	Aorta	Aorta
5	chr6:15318200-15326600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:15319000-15327600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:15319000-15328600	Weak transcription	HSMM	muscle
8	chr6:15319200-15326800	Weak transcription	Right Atrium	heart
9	chr6:15319200-15327000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:15319200-15327000	Weak transcription	Fetal Brain Female	brain
11	chr6:15319200-15328000	Weak transcription	Fetal Stomach	stomach
12	chr6:15319200-15329000	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:15319400-15335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:15319600-15326800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:15319800-15326600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:15319800-15327200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:15320000-15327000	Weak transcription	Fetal Heart	heart
18	chr6:15320200-15327600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:15320400-15328600	Weak transcription	Brain Germinal Matrix	brain
20	chr6:15322400-15326800	Enhancers	HepG2	liver
21	chr6:15322800-15327200	Weak transcription	Fetal Lung	lung
22	chr6:15323000-15326600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:15323200-15328800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:15323600-15326600	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:15323600-15326600	Weak transcription	Gastric	stomach
26	chr6:15323600-15326600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:15323600-15326800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:15323600-15327400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:15323600-15327600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:15323600-15327600	Weak transcription	Lung	lung
31	chr6:15323600-15329000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:15323600-15329600	Weak transcription	Placenta	Placenta
33	chr6:15323800-15326600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:15323800-15326600	Weak transcription	Left Ventricle	heart
35	chr6:15323800-15326600	Weak transcription	Pancreas	Pancrea
36	chr6:15323800-15326600	Weak transcription	Osteobl	bone
37	chr6:15323800-15326800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:15323800-15326800	Weak transcription	Brain Anterior Caudate	brain
39	chr6:15323800-15326800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:15323800-15327000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:15323800-15327000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:15323800-15327400	Weak transcription	NH-A	brain
43	chr6:15323800-15327600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:15323800-15327600	Weak transcription	Brain Angular Gyrus	brain
45	chr6:15323800-15327600	Weak transcription	NHDF-Ad	bronchial
46	chr6:15323800-15328400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:15323800-15328400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr6:15323800-15328800	Weak transcription	HSMMtube	muscle
49	chr6:15323800-15329000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:15323800-15330000	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links