Variant report

Variant	rs10456788
Chromosome Location	chr6:16750856-16750857
allele	A/C/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	chr6:16746939-16750864	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:16747791..16751761-chr6:16752164..16756534,5	MCF-7	breast:

Variant related genes	Relation type
ATXN1	TF binding region
ENSG00000124788	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10434861	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10456789	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456790	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194640	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs16878970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16879003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806144	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6459484	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6915772	0.86[EUR][1000 genomes]
rs9350015	1.00[CEU][hapmap];0.90[TSI][hapmap]

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	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10456788	ATXN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16732200-16754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:16737600-16759400	Weak transcription	Thymus	Thymus
3	chr6:16739000-16752200	Weak transcription	HUVEC	blood vessel
4	chr6:16741200-16758200	Enhancers	Fetal Heart	heart
5	chr6:16743000-16757200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:16743000-16759600	Weak transcription	Spleen	Spleen
7	chr6:16743800-16757200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:16745000-16759600	Weak transcription	Placenta	Placenta
9	chr6:16746000-16751600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:16746200-16751400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:16746200-16758400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:16746400-16752600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:16746400-16756800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:16746400-16758600	Weak transcription	Primary T cells from cord blood	blood
15	chr6:16746400-16758800	Weak transcription	Fetal Thymus	thymus
16	chr6:16746800-16758600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:16747000-16752600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:16747200-16751400	Weak transcription	Hela-S3	cervix
19	chr6:16748000-16751400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:16748200-16751400	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:16748200-16751400	Weak transcription	HMEC	breast
22	chr6:16748200-16754800	Genic enhancers	HepG2	liver
23	chr6:16748200-16756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:16748200-16757200	Weak transcription	Fetal Brain Male	brain
25	chr6:16748200-16758200	Weak transcription	Brain Germinal Matrix	brain
26	chr6:16748200-16758400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:16748400-16752000	Weak transcription	Stomach Mucosa	stomach
28	chr6:16748400-16753200	Weak transcription	Adipose Nuclei	Adipose
29	chr6:16748400-16758000	Weak transcription	Fetal Brain Female	brain
30	chr6:16748600-16751600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:16748600-16751800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:16748600-16752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:16748600-16752400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:16748800-16751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:16748800-16751600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:16748800-16751600	Weak transcription	Colonic Mucosa	Colon
37	chr6:16748800-16751600	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:16748800-16752000	Weak transcription	Fetal Kidney	kidney
39	chr6:16748800-16752000	Weak transcription	Psoas Muscle	Psoas
40	chr6:16748800-16753200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:16748800-16758400	Weak transcription	Gastric	stomach
42	chr6:16748800-16758600	Weak transcription	Right Atrium	heart
43	chr6:16748800-16758800	Weak transcription	Ovary	ovary
44	chr6:16748800-16759000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:16748800-16759800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:16749000-16751000	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:16749000-16751400	Weak transcription	Small Intestine	intestine
48	chr6:16749200-16751400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:16749200-16751600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:16749200-16753400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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