Variant report

Variant	rs35599677
Chromosome Location	chr12:121141458-121141459
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	POLR2A	chr12:121141260-121141779	HL-60	blood:	n/a	n/a
2	POLR2A	chr12:121141334-121141746	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:121141371-121141651	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:121141318-121141808	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:121141443-121141616	K562	blood:	n/a	n/a
6	POLR2A	chr12:121141375-121141514	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:121141278-121141778	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121140803..121142860-chr12:121453147..121455600,2	K562	blood:
2	chr12:121125276..121128582-chr12:121139011..121141679,3	MCF-7	breast:
3	chr12:121139055..121141788-chr12:121148232..121149870,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256364	TF binding region
ENSG00000175970	Chromatin interaction
ENSG00000157895	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12311479	0.93[ASN][1000 genomes]
rs12828810	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12829722	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799958	0.88[EUR][1000 genomes]
rs2014355	0.88[EUR][1000 genomes]
rs2066938	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239758	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2393778	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3021337	0.87[ASN][1000 genomes]
rs3021338	0.82[ASN][1000 genomes]
rs34030695	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34673751	0.89[EUR][1000 genomes]
rs34708625	0.88[EUR][1000 genomes]
rs34734847	0.90[ASN][1000 genomes]
rs35360964	0.88[ASN][1000 genomes]
rs35525135	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35771722	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3752531	0.90[ASN][1000 genomes]
rs3916	0.88[EUR][1000 genomes]
rs3999408	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55730005	0.90[ASN][1000 genomes]
rs56273049	0.90[ASN][1000 genomes]
rs57830821	0.94[ASN][1000 genomes]
rs60858026	1.00[ASN][1000 genomes]
rs71454661	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306541	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313271	0.90[AMR][1000 genomes];0.94[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121127600-121147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:121130200-121143000	Strong transcription	Dnd41	blood
3	chr12:121130200-121143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:121130600-121141800	Strong transcription	NHEK	skin
5	chr12:121130600-121142000	Strong transcription	Fetal Stomach	stomach
6	chr12:121130600-121142400	Strong transcription	GM12878-XiMat	blood
7	chr12:121130600-121143200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:121130800-121141600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr12:121130800-121141800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:121130800-121141800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:121130800-121141800	Strong transcription	Thymus	Thymus
12	chr12:121130800-121142000	Strong transcription	Osteobl	bone
13	chr12:121130800-121142200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:121130800-121143600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:121131000-121141600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:121131000-121142400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:121131200-121141800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:121131200-121141800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:121131200-121142000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:121131200-121143800	Strong transcription	Fetal Thymus	thymus
21	chr12:121131400-121141800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:121131400-121142200	Strong transcription	Primary T cells from cord blood	blood
23	chr12:121131600-121141800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:121131600-121141800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:121131600-121141800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:121131600-121141800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:121131800-121141600	Strong transcription	Brain Angular Gyrus	brain
28	chr12:121131800-121141600	Strong transcription	Colon Smooth Muscle	Colon
29	chr12:121131800-121141800	Strong transcription	Liver	Liver
30	chr12:121131800-121141800	Strong transcription	Fetal Brain Female	brain
31	chr12:121132000-121141800	Strong transcription	HSMMtube	muscle
32	chr12:121132200-121143600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:121132400-121141600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:121132400-121141800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:121132400-121143000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:121132600-121141800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:121132600-121141800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:121132600-121143600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:121132800-121141600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:121132800-121141800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:121133200-121142200	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr12:121134200-121142000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:121134400-121142000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:121135400-121141800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr12:121135400-121147400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:121135600-121146400	Strong transcription	Fetal Intestine Small	intestine
47	chr12:121135600-121147400	Weak transcription	Fetal Brain Male	brain
48	chr12:121136000-121141800	Strong transcription	Fetal Intestine Large	intestine
49	chr12:121136000-121142000	Enhancers	Right Atrium	heart
50	chr12:121136000-121147600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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