Variant report

Variant	rs10456791
Chromosome Location	chr6:16753352-16753353
allele	A/C
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	SIN3AK20	chr6:16753333-16753959	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr6:16752063-16754269	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr6:16752650-16754058	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:16751293-16754429	PFSK-1	brain:	n/a	n/a
5	JUND	chr6:16752206-16753616	SK-N-SH	brain:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752923 chr6:16752912-16752924
6	POLR2A	chr6:16753348-16754433	K562	blood:	n/a	n/a
7	SIN3AK20	chr6:16753245-16754028	PFSK-1	brain:	n/a	n/a
8	FOSL1	chr6:16752320-16753370	HCT-116	colon:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL137003.1-1	chr6:16753193-16753578	NONHSAT107907

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

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10434861	0.86[EUR][1000 genomes]
rs10456788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456789	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878970	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16879003	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806144	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6459484	0.86[EUR][1000 genomes]
rs6915772	0.86[EUR][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	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

No data

Chromatin state (count:117 , 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	chr6:16741200-16758200	Enhancers	Fetal Heart	heart
4	chr6:16743000-16757200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:16743000-16759600	Weak transcription	Spleen	Spleen
6	chr6:16743800-16757200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:16745000-16759600	Weak transcription	Placenta	Placenta
8	chr6:16746200-16758400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:16746400-16756800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:16746400-16758600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:16746400-16758800	Weak transcription	Fetal Thymus	thymus
12	chr6:16746800-16758600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:16748200-16754800	Genic enhancers	HepG2	liver
14	chr6:16748200-16756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:16748200-16757200	Weak transcription	Fetal Brain Male	brain
16	chr6:16748200-16758200	Weak transcription	Brain Germinal Matrix	brain
17	chr6:16748200-16758400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:16748400-16758000	Weak transcription	Fetal Brain Female	brain
19	chr6:16748800-16758400	Weak transcription	Gastric	stomach
20	chr6:16748800-16758600	Weak transcription	Right Atrium	heart
21	chr6:16748800-16758800	Weak transcription	Ovary	ovary
22	chr6:16748800-16759000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:16748800-16759800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:16749200-16753400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:16749200-16758400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:16749600-16753600	Genic enhancers	HSMM	muscle
27	chr6:16749600-16754800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:16749800-16753600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:16749800-16754000	Genic enhancers	NHDF-Ad	bronchial
30	chr6:16750000-16753800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:16750200-16753800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:16750200-16758600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:16750400-16753600	Weak transcription	Aorta	Aorta
34	chr6:16750400-16753600	Enhancers	Osteobl	bone
35	chr6:16750400-16754600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:16750400-16758600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:16750400-16758800	Weak transcription	Esophagus	oesophagus
38	chr6:16750400-16759800	Weak transcription	Lung	lung
39	chr6:16750600-16753600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:16750600-16755200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:16750600-16759000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:16750800-16753400	Enhancers	HSMMtube	muscle
43	chr6:16750800-16753600	Genic enhancers	Fetal Intestine Small	intestine
44	chr6:16751000-16756200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr6:16751000-16756800	Enhancers	Fetal Intestine Large	intestine
46	chr6:16751200-16753600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr6:16751400-16753800	Enhancers	Hela-S3	cervix
48	chr6:16751400-16753800	Enhancers	HMEC	breast
49	chr6:16751400-16754000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:16751400-16755200	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links