Variant report

Variant	rs12661489
Chromosome Location	chr6:79941833-79941834
allele	C/T
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	GATA1	chr6:79940694-79942055	PBDE	blood:	n/a	chr6:79940857-79940878 chr6:79941496-79941503 chr6:79940862-79940872 chr6:79940698-79940708 chr6:79941493-79941503 chr6:79941584-79941600 chr6:79941495-79941505 chr6:79941492-79941508 chr6:79941496-79941505 chr6:79941494-79941506

No.	Distal block	Cell Line	Cell type
1	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
2	chr6:79786645..79789143-chr6:79938512..79942027,3	MCF-7	breast:
3	chr6:79763581..79765481-chr6:79941505..79943028,2	K562	blood:
4	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:

Variant related genes	Relation type
HMGN3-AS1	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10943623	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12191682	0.88[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12214161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1414280	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4618483	0.88[ASN][1000 genomes]
rs56384338	0.88[ASN][1000 genomes]
rs6912569	0.88[ASN][1000 genomes]
rs6927281	0.81[ASN][1000 genomes]
rs7758577	0.81[ASN][1000 genomes]
rs9343883	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9343884	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9352704	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9361503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap]
rs9361505	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79907400-79942800	Weak transcription	HSMM	muscle
2	chr6:79912800-79942600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:79918200-79942000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:79925400-79942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:79925800-79942000	Weak transcription	Adipose Nuclei	Adipose
10	chr6:79925800-79942000	Weak transcription	Brain Anterior Caudate	brain
11	chr6:79925800-79942800	Weak transcription	Liver	Liver
12	chr6:79926600-79942000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:79927400-79942600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:79927800-79942000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:79927800-79942800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:79927800-79942800	Weak transcription	Primary T cells from cord blood	blood
17	chr6:79928000-79942000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:79929000-79942000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:79929000-79942000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:79931200-79942800	Weak transcription	Left Ventricle	heart
21	chr6:79931600-79942000	Weak transcription	Gastric	stomach
22	chr6:79932400-79942400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:79933800-79942600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:79934200-79942200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:79934200-79942400	Weak transcription	Primary B cells from cord blood	blood
26	chr6:79935800-79942000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:79936000-79942000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:79936200-79942200	Weak transcription	Small Intestine	intestine
29	chr6:79936200-79943000	Weak transcription	Fetal Intestine Large	intestine
30	chr6:79936200-79943000	Weak transcription	Psoas Muscle	Psoas
31	chr6:79936200-79943200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:79936800-79942800	Weak transcription	Fetal Kidney	kidney
33	chr6:79937400-79942600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:79939000-79942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:79939400-79942000	Weak transcription	Spleen	Spleen
36	chr6:79939600-79942000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:79939600-79942000	Weak transcription	Fetal Thymus	thymus
38	chr6:79939800-79942000	Active TSS	GM12878-XiMat	blood
39	chr6:79939800-79942200	Weak transcription	Fetal Brain Male	brain
40	chr6:79940000-79942000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:79940200-79942800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:79940200-79942800	Weak transcription	HMEC	breast
43	chr6:79940400-79942800	Weak transcription	NHEK	skin
44	chr6:79940600-79942000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr6:79940600-79942200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:79940600-79942800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:79940600-79942800	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:79940800-79942000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:79940800-79942400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:79940800-79942800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links