Variant report

Variant	rs7979418
Chromosome Location	chr12:46774771-46774772
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	chr12:46774708-46774820	ProgFib	skin:	n/a	n/a
2	USF1	chr12:46774709-46774999	SK-N-SH_RA	brain:	n/a	n/a
3	USF1	chr12:46774724-46774947	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46774448..46777303-chr12:46865310..46867356,2	MCF-7	breast:
2	chr12:46772586..46775083-chr12:47057146..47059153,2	MCF-7	breast:
3	chr12:46658442..46662665-chr12:46774451..46778723,6	K562	blood:

Variant related genes	Relation type
ENSG00000257261	TF binding region
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10467213	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1060735	0.85[YRI][hapmap]
rs1079780	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10880947	0.86[ASW][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs10880953	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880959	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880960	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880961	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880962	0.88[CEU][hapmap]
rs10880966	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs11183441	0.84[AMR][1000 genomes]
rs11183468	0.88[CEU][hapmap]
rs1125909	0.83[AMR][1000 genomes]
rs12099669	0.83[AMR][1000 genomes]
rs12311507	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12317787	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12320197	0.81[CEU][hapmap]
rs12813763	0.88[CEU][hapmap]
rs12814341	0.88[CEU][hapmap]
rs12816358	0.83[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12816413	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1471223	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1492892	0.90[MEX][hapmap];0.89[TSI][hapmap]
rs1492894	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1873793	0.81[CEU][hapmap]
rs2131371	0.80[AMR][1000 genomes]
rs2169030	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2172398	0.86[MEX][hapmap];0.86[TSI][hapmap]
rs2242355	0.86[MEX][hapmap]
rs2279559	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2279560	0.86[ASW][hapmap];0.85[YRI][hapmap]
rs2307061	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2408497	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs2408504	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2408505	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2408506	0.83[AMR][1000 genomes]
rs2408507	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2408508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2897968	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34119192	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3782904	0.88[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4076248	0.88[CEU][hapmap]
rs4238102	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4258438	0.81[AMR][1000 genomes]
rs4427617	0.80[AMR][1000 genomes]
rs4438106	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4547171	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4586238	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4768106	0.82[YRI][hapmap]
rs4768107	0.82[YRI][hapmap]
rs4768115	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768116	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768118	0.80[AMR][1000 genomes]
rs4768119	0.81[AMR][1000 genomes]
rs4768695	0.85[AMR][1000 genomes]
rs4768696	0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768698	0.88[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768709	0.81[AMR][1000 genomes]
rs6582622	0.82[YRI][hapmap]
rs6582656	0.88[CEU][hapmap]
rs7132228	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7312259	0.80[AMR][1000 genomes]
rs7315493	0.82[YRI][hapmap]
rs7316127	0.86[ASW][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs7316773	0.90[MEX][hapmap];0.87[TSI][hapmap]
rs7487075	0.87[CEU][hapmap]
rs7958774	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7960147	0.86[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7961994	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7968173	0.86[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7968283	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974529	0.88[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7976280	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs7979514	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7980775	0.86[ASW][hapmap];0.87[TSI][hapmap]
rs898242	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs956910	0.88[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs962683	0.82[YRI][hapmap]
rs9668077	0.83[AMR][1000 genomes]
rs9669381	0.80[AMR][1000 genomes]
rs9795971	0.83[AMR][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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46767800-46776200	Weak transcription	Small Intestine	intestine
2	chr12:46768000-46775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:46768000-46776200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:46768000-46776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:46768000-46776200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:46768000-46776200	Weak transcription	Brain Substantia Nigra	brain
7	chr12:46768000-46776200	Weak transcription	Placenta	Placenta
8	chr12:46768000-46776200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:46768000-46776400	Weak transcription	Gastric	stomach
10	chr12:46768000-46776400	Weak transcription	Left Ventricle	heart
11	chr12:46768000-46776400	Weak transcription	Psoas Muscle	Psoas
12	chr12:46768200-46775800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:46768200-46776000	Weak transcription	NH-A	brain
14	chr12:46768400-46775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:46768400-46775800	Weak transcription	A549	lung
16	chr12:46768400-46776000	Weak transcription	NHEK	skin
17	chr12:46768400-46776200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:46768400-46776200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:46768400-46776400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:46768600-46775800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:46768600-46776200	Weak transcription	Thymus	Thymus
22	chr12:46768800-46775600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:46768800-46775600	Weak transcription	NHLF	lung
24	chr12:46768800-46776000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:46768800-46776200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:46768800-46776200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:46769200-46776000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:46769200-46776200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:46769200-46776400	Weak transcription	Primary T cells from cord blood	blood
30	chr12:46770800-46775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:46771000-46776200	Weak transcription	Liver	Liver
32	chr12:46771000-46776200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:46772000-46776000	Weak transcription	NHDF-Ad	bronchial
34	chr12:46772200-46776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:46772200-46776400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:46772800-46775600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:46772800-46775600	Weak transcription	Hela-S3	cervix
38	chr12:46772800-46776200	Weak transcription	Primary B cells from cord blood	blood
39	chr12:46773000-46774800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:46773000-46776400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:46773200-46774800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:46773600-46775600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:46773600-46776600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:46773800-46776000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:46774000-46774800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:46774000-46774800	Enhancers	HepG2	liver
47	chr12:46774000-46775600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:46774000-46775600	Enhancers	K562	blood
49	chr12:46774000-46775600	Weak transcription	Osteobl	bone
50	chr12:46774000-46776000	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links