Variant report

Variant	rs5762788
Chromosome Location	chr22:29174770-29174771
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29172058..29177577-chr22:29178390..29181662,9	MCF-7	breast:
2	chr22:29174303..29175888-chr22:29187835..29189460,2	MCF-7	breast:
3	chr22:29165791..29171536-chr22:29171828..29178249,15	MCF-7	breast:
4	chr22:29174714..29176421-chr22:29187475..29189303,2	K562	blood:
5	chr22:29174755..29176682-chr22:29192335..29194092,2	K562	blood:
6	chr22:29167384..29172904-chr22:29173066..29177227,7	K562	blood:

Variant related genes	Relation type
ENSG00000159873	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs12165962	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs12628211	0.94[ASN][1000 genomes]
rs132531	0.89[JPT][hapmap];0.86[MEX][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];0.86[MEX][hapmap]
rs2064261	0.89[JPT][hapmap];0.95[MEX][hapmap]
rs2097461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2213645	0.84[JPT][hapmap]
rs2239815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269577	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[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];0.89[ASN][1000 genomes]
rs35259224	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788409	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs469989	0.86[CEU][hapmap]
rs469990	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap]
rs469991	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs4822998	0.82[JPT][hapmap]
rs5752795	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752798	0.93[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];0.84[ASN][1000 genomes]
rs5752804	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752807	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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];0.96[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];0.96[ASN][1000 genomes]
rs5752813	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762784	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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762803	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762815	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762824	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762825	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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];0.97[ASN][1000 genomes]
rs6005867	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005869	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6005872	0.98[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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005892	0.84[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];0.86[MEX][hapmap]
rs6005916	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005929	0.82[ASN][1000 genomes]
rs6519766	0.89[JPT][hapmap];0.95[MEX][hapmap]
rs7287124	0.94[ASN][1000 genomes]
rs7287806	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7287918	0.89[JPT][hapmap];0.95[MEX][hapmap]
rs763073	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8137969	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9620841	0.89[JPT][hapmap];0.95[MEX][hapmap]
rs9625566	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9625588	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs5762788	GAL3ST1	cis	cerebellum	SCAN
rs5762788	CCDC117	Cis_1M	lymphoblastoid	RTeQTL
rs5762788	MN1	cis	cerebellum	SCAN
rs5762788	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs5762788	SEZ6L	cis	cerebellum	SCAN
rs5762788	BEND4	trans	parietal	SCAN
rs5762788	XBP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
3	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
4	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29170000-29174800	Weak transcription	K562	blood
6	chr22:29170000-29176400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr22:29170000-29176400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:29170000-29177600	Weak transcription	Aorta	Aorta
9	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
13	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr22:29170200-29175600	Weak transcription	NHDF-Ad	bronchial
15	chr22:29170200-29177800	Weak transcription	HMEC	breast
16	chr22:29170200-29178000	Weak transcription	Brain Anterior Caudate	brain
17	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
19	chr22:29170400-29175400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr22:29170400-29175600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr22:29170400-29177800	Strong transcription	Fetal Intestine Large	intestine
22	chr22:29170400-29183800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr22:29170400-29184000	Strong transcription	Fetal Muscle Leg	muscle
24	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:29170600-29184600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr22:29170600-29184800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr22:29170800-29175000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr22:29170800-29175000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr22:29170800-29175000	Weak transcription	Psoas Muscle	Psoas
33	chr22:29170800-29179800	Weak transcription	Fetal Brain Male	brain
34	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr22:29171000-29174800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr22:29171000-29175400	Weak transcription	Colon Smooth Muscle	Colon
37	chr22:29171000-29175600	Strong transcription	Fetal Intestine Small	intestine
38	chr22:29171000-29175800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:29171000-29176400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr22:29171000-29176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr22:29171000-29178000	Weak transcription	Brain Angular Gyrus	brain
42	chr22:29171000-29179600	Weak transcription	Small Intestine	intestine
43	chr22:29171000-29185600	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr22:29171200-29174800	Strong transcription	Fetal Lung	lung
45	chr22:29171200-29176400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr22:29171200-29177000	Weak transcription	Brain Hippocampus Middle	brain
47	chr22:29171200-29178600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr22:29171200-29179000	Weak transcription	Brain Substantia Nigra	brain
49	chr22:29171200-29179200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr22:29171200-29186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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