Variant report

Variant	rs1071962
Chromosome Location	chr22:30224141-30224142
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	GATA3	chr22:30223514-30224186	SK-N-SH	brain:	n/a	chr22:30224043-30224053 chr22:30224169-30224179
2	POLR2A	chr22:30223582-30224224	H1-neurons	neurons:	n/a	n/a
3	GATA2	chr22:30223469-30224155	HUVEC	blood vessel:	n/a	chr22:30224043-30224053
4	POLR2A	chr22:30223308-30224198	HepG2	liver:	n/a	n/a
5	POLR2A	chr22:30223613-30224250	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:30223824..30225388-chr22:30399596..30401102,2	K562	blood:
2	chr22:30221897..30227952-chr22:30230604..30235599,8	MCF-7	breast:
3	chr22:30222485..30225324-chr22:30399602..30401589,2	K562	blood:

Variant related genes	Relation type
ASCC2	TF binding region
ENSG00000100325	Chromatin interaction
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12158466	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12159277	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12627866	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12628028	0.92[ASN][1000 genomes]
rs12628545	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs14115	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16987142	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16988049	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17711461	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17711508	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2018808	0.81[ASN][1000 genomes]
rs2240364	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2240365	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2240366	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.88[ASN][1000 genomes]
rs249399	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs249402	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28730892	0.88[ASN][1000 genomes]
rs36571	1.00[YRI][hapmap]
rs57122143	0.92[ASN][1000 genomes]
rs58015017	0.92[ASN][1000 genomes]
rs59394320	0.92[ASN][1000 genomes]
rs5997519	0.81[ASN][1000 genomes]
rs5997520	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs5997524	0.85[ASN][1000 genomes]
rs6006242	1.00[JPT][hapmap]
rs6006247	0.81[ASN][1000 genomes]
rs6006249	0.81[ASN][1000 genomes]
rs6006250	0.81[ASN][1000 genomes]
rs6006262	0.88[ASN][1000 genomes]
rs60805530	1.00[ASN][1000 genomes]
rs61413958	0.81[ASN][1000 genomes]
rs61616383	0.81[ASN][1000 genomes]
rs7285660	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7285800	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7287777	0.92[ASN][1000 genomes]
rs7289250	0.88[ASN][1000 genomes]
rs7290420	0.90[GIH][hapmap]
rs73392899	0.88[ASN][1000 genomes]
rs73394814	0.92[ASN][1000 genomes]
rs73394831	0.92[ASN][1000 genomes]
rs73394838	1.00[ASN][1000 genomes]
rs737721	0.81[ASN][1000 genomes]
rs737728	0.81[ASN][1000 genomes]
rs740116	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1071962	C22orf31	cis	parietal	SCAN
rs1071962	C22orf42	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
3	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
4	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr22:30203600-30233400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:30208800-30231000	Strong transcription	Brain Germinal Matrix	brain
9	chr22:30208800-30231200	Strong transcription	Lung	lung
10	chr22:30208800-30233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:30209000-30227600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr22:30209800-30233600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr22:30213600-30226000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr22:30215000-30230800	Strong transcription	Fetal Brain Female	brain
15	chr22:30215200-30233200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:30216400-30226200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:30218000-30225000	Strong transcription	Fetal Intestine Large	intestine
18	chr22:30218000-30230600	Strong transcription	Fetal Thymus	thymus
19	chr22:30218000-30231000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr22:30218200-30232200	Strong transcription	Fetal Intestine Small	intestine
21	chr22:30218400-30225800	Weak transcription	Brain Angular Gyrus	brain
22	chr22:30218400-30233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr22:30218600-30226000	Strong transcription	Liver	Liver
24	chr22:30218600-30230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:30218600-30233400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr22:30219000-30232000	Weak transcription	Fetal Brain Male	brain
27	chr22:30219600-30226000	Weak transcription	A549	lung
28	chr22:30219600-30233400	Weak transcription	Fetal Kidney	kidney
29	chr22:30220000-30231600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:30220600-30225000	Strong transcription	NHEK	skin
31	chr22:30220600-30227200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr22:30221400-30226000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr22:30221400-30226600	Weak transcription	HUVEC	blood vessel
34	chr22:30221400-30227400	Weak transcription	Brain Substantia Nigra	brain
35	chr22:30221400-30233400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:30221600-30225800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr22:30221600-30225800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr22:30221600-30225800	Weak transcription	HepG2	liver
39	chr22:30221600-30227200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr22:30221600-30227400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr22:30221600-30227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr22:30221600-30233400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr22:30221800-30224400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr22:30221800-30225000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr22:30221800-30225000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr22:30221800-30225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr22:30221800-30226000	Weak transcription	Aorta	Aorta
48	chr22:30221800-30226000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr22:30221800-30226000	Weak transcription	Gastric	stomach
50	chr22:30221800-30226000	Weak transcription	Right Ventricle	heart

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