Variant report

Variant	rs5762410
Chromosome Location	chr22:28326657-28326658
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	FOS	chr22:28326255-28327154	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr22:28326654-28326773	GM12878	blood:	n/a	n/a
3	STAT3	chr22:28326327-28326941	MCF10A-Er-Src	breast:	n/a	chr22:28326618-28326629
4	STAT3	chr22:28326378-28326909	MCF10A-Er-Src	breast:	n/a	chr22:28326618-28326629
5	POLR2A	chr22:28326283-28326879	MCF10A-Er-Src	breast:	n/a	n/a
6	TCF12	chr22:28326255-28326773	SK-N-SH	brain:	n/a	n/a
7	MYC	chr22:28326442-28327033	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr22:28326634-28327185	IMR90	lung:	n/a	chr22:28327009-28327020
9	STAT3	chr22:28326309-28327054	MCF10A-Er-Src	breast:	n/a	chr22:28326618-28326629
10	MYC	chr22:28326361-28326821	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr22:28326355-28326874	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr22:28326304-28326936	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr22:28326350-28327109	MCF10A-Er-Src	breast:	n/a	chr22:28326618-28326629
14	POLR2A	chr22:28326439-28326959	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr22:28326346-28326863	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28313170..28318455-chr22:28322115..28328804,10	MCF-7	breast:

Variant related genes	Relation type
TTC28-AS1	TF binding region
ENSG00000235954	Chromatin interaction
ENSG00000180957	Chromatin interaction
ENSG00000264073	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12160891	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs130413	0.89[CHB][hapmap]
rs2073028	0.93[JPT][hapmap]
rs2143180	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267125	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2345019	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28372773	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752651	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5752670	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762395	0.81[ASN][1000 genomes]
rs5762396	0.81[ASN][1000 genomes]
rs5762398	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762400	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5762404	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762428	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5762448	0.89[CHB][hapmap]
rs5997318	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6005672	0.82[AFR][1000 genomes]
rs6005674	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714743	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73166732	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28316200-28328400	Weak transcription	Aorta	Aorta
2	chr22:28316200-28337400	Weak transcription	Ovary	ovary
3	chr22:28316400-28327000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:28316400-28328200	Weak transcription	Left Ventricle	heart
5	chr22:28316400-28329000	Weak transcription	Pancreas	Pancrea
6	chr22:28316400-28329000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr22:28316400-28335000	Weak transcription	Colonic Mucosa	Colon
8	chr22:28316400-28336800	Weak transcription	Fetal Muscle Leg	muscle
9	chr22:28316400-28342600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr22:28316400-28358600	Weak transcription	Placenta	Placenta
11	chr22:28316400-28370200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr22:28316400-28376800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:28316400-28378000	Weak transcription	Esophagus	oesophagus
14	chr22:28316600-28328600	Weak transcription	Stomach Mucosa	stomach
15	chr22:28316600-28348400	Weak transcription	Brain Substantia Nigra	brain
16	chr22:28316800-28329000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr22:28316800-28333800	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:28316800-28336600	Weak transcription	Fetal Intestine Large	intestine
19	chr22:28316800-28340400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr22:28317000-28327400	Weak transcription	Adipose Nuclei	Adipose
21	chr22:28317000-28338800	Weak transcription	Fetal Intestine Small	intestine
22	chr22:28317000-28340800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr22:28317000-28348200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr22:28317200-28336600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr22:28317600-28329000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr22:28317600-28340800	Weak transcription	Thymus	Thymus
27	chr22:28317800-28342600	Weak transcription	Small Intestine	intestine
28	chr22:28317800-28345200	Weak transcription	HepG2	liver
29	chr22:28318600-28332400	Weak transcription	K562	blood
30	chr22:28318800-28382000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr22:28319400-28334000	Weak transcription	Fetal Stomach	stomach
32	chr22:28319600-28340800	Weak transcription	Fetal Thymus	thymus
33	chr22:28319600-28358000	Weak transcription	Brain Germinal Matrix	brain
34	chr22:28319600-28383000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr22:28320800-28347800	Weak transcription	HUVEC	blood vessel
36	chr22:28321000-28327600	Weak transcription	Liver	Liver
37	chr22:28321000-28354800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr22:28321200-28329000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr22:28321200-28358400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr22:28321400-28340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr22:28321400-28379000	Weak transcription	Primary B cells from cord blood	blood
42	chr22:28321600-28332200	Weak transcription	Fetal Brain Female	brain
43	chr22:28321600-28345000	Weak transcription	Fetal Lung	lung
44	chr22:28321800-28342800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr22:28322000-28365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr22:28322000-28366200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr22:28322200-28339600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr22:28322400-28329000	Weak transcription	Primary T cells from cord blood	blood
49	chr22:28322600-28329400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr22:28323000-28331000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links