Variant report

Variant	rs7306541
Chromosome Location	chr12:121130046-121130047
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	BCL3	chr12:121129956-121131200	A549	lung:	n/a	chr12:121130107-121130116
2	SP1	chr12:121129846-121130842	A549	lung:	n/a	n/a
3	GATA3	chr12:121129900-121131147	A549	lung:	n/a	n/a
4	ATF3	chr12:121129986-121130724	A549	lung:	n/a	n/a
5	EP300	chr12:121129878-121130892	A549	lung:	n/a	chr12:121130360-121130370
6	FOSL2	chr12:121130012-121130858	A549	lung:	n/a	n/a
7	EP300	chr12:121129887-121130857	A549	lung:	n/a	chr12:121130360-121130370
8	SIN3AK20	chr12:121129940-121130769	A549	lung:	n/a	n/a
9	TCF12	chr12:121129857-121130992	A549	lung:	n/a	n/a
10	SP1	chr12:121129818-121130884	A549	lung:	n/a	n/a
11	MAX	chr12:121129884-121130960	A549	lung:	n/a	chr12:121130523-121130534 chr12:121130523-121130534
12	SIN3AK20	chr12:121130033-121130694	A549	lung:	n/a	n/a
13	CEBPB	chr12:121129785-121130777	A549	lung:	n/a	chr12:121129913-121129924
14	REST	chr12:121129935-121131015	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121127233..121131774-chr12:121146015..121149455,5	MCF-7	breast:
2	chr12:121092373..121094051-chr12:121128187..121130355,2	MCF-7	breast:
3	chr12:121128598..121131378-chr12:121142040..121143642,2	K562	blood:
4	chr12:121128710..121131143-chr12:121131360..121132906,2	MCF-7	breast:

Variant related genes	Relation type
MLEC	TF binding region
ENSG00000157782	Chromatin interaction
ENSG00000175970	Chromatin interaction
ENSG00000110917	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10431386	0.81[CEU][hapmap]
rs12311479	0.93[ASN][1000 genomes]
rs12828810	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12829722	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799958	0.86[EUR][1000 genomes]
rs2014355	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2066938	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239758	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2393778	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3021337	0.87[ASN][1000 genomes]
rs3021338	0.82[ASN][1000 genomes]
rs34030695	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34673751	0.87[EUR][1000 genomes]
rs34708625	0.86[EUR][1000 genomes]
rs34734847	0.90[ASN][1000 genomes]
rs35360964	0.88[ASN][1000 genomes]
rs35525135	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35599677	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35771722	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3752531	0.90[ASN][1000 genomes]
rs3916	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3999408	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55730005	0.90[ASN][1000 genomes]
rs56273049	0.90[ASN][1000 genomes]
rs57830821	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60858026	1.00[ASN][1000 genomes]
rs71454661	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313271	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 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	chr12:121126200-121130400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:121126800-121131000	Enhancers	Placenta	Placenta
3	chr12:121127000-121131400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:121127200-121131000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:121127400-121130200	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:121127400-121130800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:121127400-121131000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:121127400-121131800	Weak transcription	Fetal Brain Female	brain
9	chr12:121127600-121130400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:121127600-121130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:121127600-121130400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:121127600-121130400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:121127600-121130600	Enhancers	Fetal Lung	lung
14	chr12:121127600-121130600	Enhancers	Psoas Muscle	Psoas
15	chr12:121127600-121130800	Enhancers	Left Ventricle	heart
16	chr12:121127600-121131000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:121127600-121131000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:121127600-121131000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:121127600-121131000	Weak transcription	Aorta	Aorta
20	chr12:121127600-121131000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr12:121127600-121131000	Enhancers	HepG2	liver
22	chr12:121127600-121131600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:121127600-121131600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:121127600-121131600	Enhancers	Adipose Nuclei	Adipose
25	chr12:121127600-121132000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:121127600-121132000	Weak transcription	Esophagus	oesophagus
27	chr12:121127600-121132000	Weak transcription	HSMM	muscle
28	chr12:121127600-121132600	Weak transcription	Fetal Brain Male	brain
29	chr12:121127600-121147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:121127800-121130200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:121127800-121130600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:121127800-121130600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:121127800-121130800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:121127800-121130800	Weak transcription	Osteobl	bone
35	chr12:121127800-121131000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:121127800-121131000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:121127800-121131400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr12:121127800-121131400	Weak transcription	Brain Germinal Matrix	brain
39	chr12:121127800-121131600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:121127800-121131800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:121127800-121132000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:121127800-121132000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:121127800-121132000	Weak transcription	HMEC	breast
44	chr12:121127800-121132000	Weak transcription	HSMMtube	muscle
45	chr12:121127800-121132200	Weak transcription	NH-A	brain
46	chr12:121127800-121135000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:121128000-121130200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:121128000-121130400	Weak transcription	Primary B cells from cord blood	blood
49	chr12:121128000-121130600	Enhancers	Fetal Intestine Large	intestine
50	chr12:121128000-121130600	Weak transcription	Fetal Stomach	stomach

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