Variant report

Variant	rs1222
Chromosome Location	chr22:29185113-29185114
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29145305..29148162-chr22:29185055..29187826,2	K562	blood:
2	chr22:29136633..29138535-chr22:29184332..29186376,2	MCF-7	breast:
3	chr22:29151815..29154169-chr22:29184646..29186865,2	MCF-7	breast:
4	chr22:29171571..29173553-chr22:29184100..29185761,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs13053879	0.85[EUR][1000 genomes]
rs13056243	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs13056546	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13058031	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap]
rs16986825	0.94[CEU][hapmap];0.83[TSI][hapmap]
rs16986838	0.94[CEU][hapmap]
rs16986861	0.94[CEU][hapmap]
rs16986864	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs16987024	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987027	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235431	0.93[EUR][1000 genomes]
rs2236141	0.88[EUR][1000 genomes]
rs2267131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269578	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28458474	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881634	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34206997	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34298044	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34573837	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34718288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34751572	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35017742	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35829597	0.86[EUR][1000 genomes]
rs35905502	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36112964	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4055	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs5752790	0.88[EUR][1000 genomes]
rs5752794	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752796	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752797	0.83[CEU][hapmap]
rs5752802	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752806	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752810	0.83[CEU][hapmap]
rs5752811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752815	0.83[CEU][hapmap]
rs5752816	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762767	0.94[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs5762774	0.88[EUR][1000 genomes]
rs5762780	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs5762794	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762799	0.83[CEU][hapmap]
rs5762809	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5762812	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762814	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762817	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762818	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762819	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762820	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762821	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762822	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762823	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762839	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs5762848	0.83[CEU][hapmap]
rs5762857	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60468718	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66471734	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71327317	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170633	0.91[EUR][1000 genomes]
rs739196	0.94[CEU][hapmap];0.83[TSI][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	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
4	nsv964711	chr22:29181980-29185333	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1222	FLJ33814	cis	multi-tissue	Pritchard
rs1222	MN1	cis	cerebellum	SCAN
rs1222	RGL4	cis	parietal	SCAN
rs1222	SUSD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
3	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr22:29171000-29185600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr22:29171200-29186800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:29171200-29188600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:29171400-29186000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr22:29171800-29186200	Strong transcription	Fetal Thymus	thymus
14	chr22:29172400-29186200	Strong transcription	Placenta	Placenta
15	chr22:29173200-29185600	Strong transcription	Left Ventricle	heart
16	chr22:29173800-29185600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:29173800-29193000	Weak transcription	Right Atrium	heart
18	chr22:29175000-29186000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr22:29175400-29185600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr22:29175600-29185800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr22:29175800-29185200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr22:29175800-29185600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr22:29175800-29186200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr22:29176400-29185200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:29176400-29185600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr22:29176400-29186000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr22:29176600-29185600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr22:29176800-29190200	Weak transcription	Hela-S3	cervix
29	chr22:29177800-29185400	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr22:29178000-29185400	Strong transcription	NH-A	brain
31	chr22:29178000-29185600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr22:29178400-29185600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:29178800-29185200	Strong transcription	NHDF-Ad	bronchial
34	chr22:29178800-29185600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr22:29178800-29185600	Strong transcription	HSMM	muscle
36	chr22:29178800-29185600	Strong transcription	Osteobl	bone
37	chr22:29180200-29185600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:29180400-29186200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:29180400-29191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr22:29180600-29186000	Strong transcription	Fetal Lung	lung
41	chr22:29180600-29191000	Weak transcription	Small Intestine	intestine
42	chr22:29180800-29185600	Strong transcription	Liver	Liver
43	chr22:29180800-29189800	Weak transcription	HMEC	breast
44	chr22:29180800-29190200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr22:29181200-29186000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr22:29181600-29185600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr22:29181600-29191000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr22:29181800-29186400	Strong transcription	Fetal Intestine Large	intestine
49	chr22:29182000-29188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr22:29182000-29191000	Weak transcription	Fetal Brain Male	brain

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