Variant report

Variant	rs11057522
Chromosome Location	chr12:122807572-122807573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122806652..122808672-chr12:122809920..122812216,3	K562	blood:
2	chr12:122800308..122802580-chr12:122806199..122807965,2	K562	blood:
3	chr12:122805766..122808468-chr12:122824951..122827669,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10161184	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10161488	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10773090	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10773108	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10773117	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10846714	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10846912	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs11057514	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057686	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057813	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11057819	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1129167	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11503023	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12812332	0.82[CEU][hapmap]
rs12818177	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12828876	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12829449	0.81[EUR][1000 genomes]
rs1392142	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs1532579	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs1553178	0.85[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3825096	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs4758665	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758692	0.81[GIH][hapmap]
rs4758693	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4758695	0.85[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs61021925	0.81[EUR][1000 genomes]
rs6488947	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7313121	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313284	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7959550	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7961258	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7972832	0.82[EUR][1000 genomes]
rs7973480	0.82[EUR][1000 genomes]
rs7974160	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7975492	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978636	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs868181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788228	0.95[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11057522	NME2P1	cis	parietal	SCAN
rs11057522	DYNLL1	cis	parietal	SCAN
rs11057522	NME2P1	cis	cerebellum	SCAN
rs11057522	GATC	cis	cerebellum	SCAN
rs11057522	CCDC62	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122752400-122810400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:122754600-122822400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr12:122763600-122812000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:122770200-122821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:122770400-122821800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:122775600-122833600	Strong transcription	Liver	Liver
7	chr12:122776000-122822200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:122778000-122808800	Weak transcription	Fetal Heart	heart
9	chr12:122780000-122827200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:122780400-122812000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:122780400-122812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:122781400-122821400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:122785800-122827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:122787200-122809000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:122788200-122821200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:122790000-122810800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
18	chr12:122792400-122819800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:122793400-122810600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:122794600-122811800	Weak transcription	Small Intestine	intestine
21	chr12:122794600-122832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:122795600-122810600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:122795800-122818200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:122796200-122808600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:122796800-122808600	Strong transcription	Fetal Stomach	stomach
26	chr12:122797000-122808800	Strong transcription	Fetal Intestine Small	intestine
27	chr12:122797200-122814000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:122797200-122822400	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:122797400-122808600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:122797600-122809000	Strong transcription	Primary T cells from cord blood	blood
31	chr12:122798600-122813200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:122798800-122809200	Strong transcription	Fetal Intestine Large	intestine
33	chr12:122800200-122810800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:122800400-122809800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:122800400-122820600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:122802000-122810400	Weak transcription	Brain Substantia Nigra	brain
37	chr12:122802200-122812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:122802400-122810400	Weak transcription	Fetal Lung	lung
39	chr12:122802800-122810400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:122803800-122812000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:122804000-122808000	Weak transcription	HMEC	breast
42	chr12:122804000-122811600	Weak transcription	Fetal Brain Male	brain
43	chr12:122804000-122811800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:122804000-122817000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:122804000-122817800	Weak transcription	Stomach Mucosa	stomach
46	chr12:122804200-122807800	Weak transcription	Colonic Mucosa	Colon
47	chr12:122804200-122808000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:122804200-122808000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:122804200-122808200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:122804200-122810000	Weak transcription	Hela-S3	cervix

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