Variant report

Variant	rs7287806
Chromosome Location	chr22:29213011-29213012
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	POLR2A	chr22:29212871-29213131	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
2	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
3	chr22:29167462..29171106-chr22:29208719..29213065,6	MCF-7	breast:
4	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	TF binding region
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12165962	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]
rs12628211	0.96[ASN][1000 genomes]
rs132531	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs132533	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs132534	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs132536	0.89[JPT][hapmap]
rs132539	0.85[TSI][hapmap]
rs132548	0.83[CEU][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.95[YRI][hapmap]
rs2064261	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs2097461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2213645	0.84[JPT][hapmap]
rs2239815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269577	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2347447	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2881635	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35259224	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3788409	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469989	0.82[CEU][hapmap]
rs469990	0.89[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs469991	0.89[JPT][hapmap]
rs4822998	0.82[JPT][hapmap]
rs5752795	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752798	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752801	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5752804	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752807	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752809	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752812	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752813	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762784	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]
rs5762788	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]
rs5762795	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762803	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs5762815	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762824	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762825	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762853	0.85[ASN][1000 genomes]
rs5762854	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762859	0.80[ASN][1000 genomes]
rs5762863	0.86[ASN][1000 genomes]
rs5762864	0.86[ASN][1000 genomes]
rs5762865	0.81[EUR][1000 genomes]
rs5762867	0.80[ASN][1000 genomes]
rs5762870	0.80[AMR][1000 genomes]
rs5762874	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762881	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762882	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762936	0.84[JPT][hapmap]
rs5997408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005867	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005869	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6005872	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005881	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005892	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005915	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs6005916	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005927	0.83[ASN][1000 genomes]
rs6005929	0.85[ASN][1000 genomes]
rs6519766	0.89[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs7287124	0.96[ASN][1000 genomes]
rs7287918	0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs763073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8137969	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9620841	0.89[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs9625566	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9625588	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9625619	0.83[CEU][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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
rs7287806	GAL3ST1	cis	cerebellum	SCAN
rs7287806	XBP1	cis	cerebellum	SCAN
rs7287806	SEZ6L	cis	cerebellum	SCAN
rs7287806	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs7287806	MN1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29214200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr22:29197400-29214400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:29197800-29214200	Weak transcription	Right Ventricle	heart
6	chr22:29198000-29225200	Weak transcription	HSMM	muscle
7	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
8	chr22:29198400-29214000	Weak transcription	Colonic Mucosa	Colon
9	chr22:29198400-29214400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:29198400-29215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr22:29198600-29214200	Weak transcription	Colon Smooth Muscle	Colon
13	chr22:29198600-29214400	Weak transcription	Aorta	Aorta
14	chr22:29198600-29214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr22:29198600-29219400	Weak transcription	NHLF	lung
16	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr22:29198600-29225200	Weak transcription	Osteobl	bone
18	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
19	chr22:29198800-29214200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr22:29198800-29214400	Weak transcription	Fetal Heart	heart
21	chr22:29198800-29230800	Weak transcription	NHEK	skin
22	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:29204800-29214600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:29205000-29214200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr22:29205200-29214400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr22:29205200-29218800	Weak transcription	Brain Hippocampus Middle	brain
27	chr22:29205400-29217000	Weak transcription	Gastric	stomach
28	chr22:29205400-29225600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:29206200-29215600	Enhancers	Stomach Mucosa	stomach
30	chr22:29207000-29213200	Enhancers	Pancreas	Pancrea
31	chr22:29207400-29214200	Weak transcription	Small Intestine	intestine
32	chr22:29207400-29214400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr22:29207800-29214400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr22:29208200-29214200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr22:29208200-29221000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr22:29208400-29213200	Enhancers	Primary T cells from cord blood	blood
37	chr22:29208400-29214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr22:29208400-29214200	Weak transcription	K562	blood
39	chr22:29208400-29217000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr22:29208600-29214000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr22:29208600-29214200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr22:29208600-29214200	Weak transcription	Esophagus	oesophagus
43	chr22:29209200-29214200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr22:29210000-29214200	Weak transcription	Fetal Lung	lung
45	chr22:29210000-29214200	Weak transcription	Right Atrium	heart
46	chr22:29210000-29214400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr22:29210200-29213800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr22:29210200-29214000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr22:29210200-29214200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:29210200-29214200	Weak transcription	Fetal Kidney	kidney

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