Variant report

Variant	rs5762784
Chromosome Location	chr22:29171298-29171299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
2	chr22:29168270..29171327-chr22:29194850..29198169,6	MCF-7	breast:
3	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
4	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
5	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
6	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000183765	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12165962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs12628211	0.93[ASN][1000 genomes]
rs132531	0.89[JPT][hapmap]
rs132533	0.89[JPT][hapmap]
rs132536	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs132539	0.83[CEU][hapmap]
rs132548	0.89[JPT][hapmap]
rs2064261	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs2097461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2213645	0.84[JPT][hapmap]
rs2239815	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269577	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2347447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2881635	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35259224	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788409	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469989	0.86[CEU][hapmap]
rs469990	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs469991	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs4822998	0.82[JPT][hapmap]
rs5752795	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752798	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752801	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752804	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752807	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752813	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762795	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762803	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762815	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762824	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762825	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762853	0.82[ASN][1000 genomes]
rs5762854	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5762863	0.83[ASN][1000 genomes]
rs5762864	0.83[ASN][1000 genomes]
rs5762874	0.89[JPT][hapmap]
rs5762881	0.89[JPT][hapmap]
rs5762882	0.89[JPT][hapmap]
rs5997408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005867	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005869	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6005872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005881	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005892	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005915	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6005916	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005929	0.81[ASN][1000 genomes]
rs6519766	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs7287124	0.93[ASN][1000 genomes]
rs7287806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7287918	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs763073	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8137969	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9620841	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs9625566	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9625588	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9625619	0.89[JPT][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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs5762784	MN1	cis	cerebellum	SCAN
rs5762784	SEZ6L	cis	cerebellum	SCAN
rs5762784	BEND4	trans	parietal	SCAN
rs5762784	GAL3ST1	cis	cerebellum	SCAN
rs5762784	XBP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29172000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:29169800-29172000	Weak transcription	Gastric	stomach
3	chr22:29169800-29172000	Weak transcription	Lung	lung
4	chr22:29169800-29172000	Weak transcription	Spleen	Spleen
5	chr22:29169800-29173000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:29169800-29173600	Weak transcription	Esophagus	oesophagus
7	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
9	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
10	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr22:29170000-29171400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:29170000-29171400	Enhancers	Adipose Nuclei	Adipose
13	chr22:29170000-29171800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr22:29170000-29171800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr22:29170000-29172000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr22:29170000-29172000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr22:29170000-29172000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr22:29170000-29172000	Weak transcription	Ovary	ovary
19	chr22:29170000-29172000	Weak transcription	Right Atrium	heart
20	chr22:29170000-29172400	Strong transcription	NH-A	brain
21	chr22:29170000-29173000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:29170000-29174800	Weak transcription	K562	blood
23	chr22:29170000-29176400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr22:29170000-29176400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr22:29170000-29177600	Weak transcription	Aorta	Aorta
26	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
30	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr22:29170200-29171400	Weak transcription	NHLF	lung
32	chr22:29170200-29172400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:29170200-29172400	Genic enhancers	Placenta	Placenta
34	chr22:29170200-29175600	Weak transcription	NHDF-Ad	bronchial
35	chr22:29170200-29177800	Weak transcription	HMEC	breast
36	chr22:29170200-29178000	Weak transcription	Brain Anterior Caudate	brain
37	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
39	chr22:29170400-29171400	Transcr. at gene 5' and 3'	Dnd41	blood
40	chr22:29170400-29171600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr22:29170400-29171800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr22:29170400-29172000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:29170400-29172200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr22:29170400-29172200	Genic enhancers	HepG2	liver
45	chr22:29170400-29172400	Strong transcription	HSMMtube	muscle
46	chr22:29170400-29173800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr22:29170400-29173800	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr22:29170400-29173800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr22:29170400-29174000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr22:29170400-29174400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links