Variant report

Variant	rs13220697
Chromosome Location	chr6:79942361-79942362
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	RFX5	chr6:79942075-79945226	SK-N-SH	brain:	n/a	chr6:79944581-79944596

No.	Distal block	Cell Line	Cell type
1	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
2	chr6:79763581..79765481-chr6:79941505..79943028,2	K562	blood:
3	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: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13200164	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13203405	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13203510	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13209338	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13209772	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13210296	0.82[CEU][hapmap];0.98[EUR][1000 genomes]
rs13210935	0.98[EUR][1000 genomes]
rs13212378	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13213305	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217071	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217706	0.82[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28360569	0.98[EUR][1000 genomes]
rs34057607	0.96[EUR][1000 genomes]
rs34493475	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34688736	0.94[EUR][1000 genomes]
rs35034704	0.82[AFR][1000 genomes]
rs35099838	0.92[EUR][1000 genomes]
rs35201024	0.98[EUR][1000 genomes]
rs35233121	0.98[EUR][1000 genomes]
rs35237040	0.94[EUR][1000 genomes]
rs35332837	0.98[EUR][1000 genomes]
rs35742788	0.98[EUR][1000 genomes]
rs35838792	0.89[EUR][1000 genomes]
rs36116051	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55773960	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66513375	0.98[EUR][1000 genomes]
rs66633427	0.98[EUR][1000 genomes]
rs66809524	0.98[EUR][1000 genomes]
rs66869917	0.98[EUR][1000 genomes]
rs72893783	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9448670	0.92[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13220697	HMGN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 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	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:79925400-79942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:79925800-79942800	Weak transcription	Liver	Liver
9	chr6:79927400-79942600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr6:79927800-79942800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:79927800-79942800	Weak transcription	Primary T cells from cord blood	blood
12	chr6:79931200-79942800	Weak transcription	Left Ventricle	heart
13	chr6:79932400-79942400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:79933800-79942600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:79934200-79942400	Weak transcription	Primary B cells from cord blood	blood
16	chr6:79936200-79943000	Weak transcription	Fetal Intestine Large	intestine
17	chr6:79936200-79943000	Weak transcription	Psoas Muscle	Psoas
18	chr6:79936200-79943200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:79936800-79942800	Weak transcription	Fetal Kidney	kidney
20	chr6:79937400-79942600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:79939000-79942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:79940200-79942800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:79940200-79942800	Weak transcription	HMEC	breast
24	chr6:79940400-79942800	Weak transcription	NHEK	skin
25	chr6:79940600-79942800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:79940600-79942800	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:79940800-79942400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:79940800-79942800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:79940800-79942800	Enhancers	Brain Hippocampus Middle	brain
30	chr6:79940800-79942800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr6:79940800-79942800	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr6:79940800-79942800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:79940800-79943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:79941000-79942400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:79941000-79942800	Enhancers	HepG2	liver
36	chr6:79941000-79943000	Enhancers	Fetal Heart	heart
37	chr6:79941200-79942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:79941200-79942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:79941200-79942800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr6:79941200-79943200	Weak transcription	Pancreas	Pancrea
41	chr6:79941400-79942400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr6:79941400-79942600	Enhancers	Duodenum Mucosa	Duodenum
43	chr6:79941400-79942800	Weak transcription	Fetal Lung	lung
44	chr6:79941400-79942800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr6:79941600-79942400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr6:79941600-79942400	Enhancers	K562	blood
47	chr6:79941600-79942800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:79941600-79942800	Enhancers	Colon Smooth Muscle	Colon
49	chr6:79941600-79942800	Weak transcription	Thymus	Thymus
50	chr6:79941600-79943000	Enhancers	Fetal Intestine Small	intestine

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