Variant report

Variant	rs360142
Chromosome Location	chr11:9786017-9786018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9779761..9781749-chr11:9784316..9786862,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SWAP70-4	chr11:9785967-9786486	predAs_chen_BG207485_1

Variant related genes	Relation type
ENSG00000245522	Chromatin interaction
ENSG00000246273	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10118	0.84[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs10770062	0.80[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1392026	0.98[ASN][1000 genomes]
rs183110	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1875030	0.97[ASN][1000 genomes]
rs2173030	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645017	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2645029	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360120	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360124	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360127	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360129	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360130	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360131	0.91[ASN][1000 genomes]
rs360132	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs360140	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360141	0.98[ASN][1000 genomes]
rs360143	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360150	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360151	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360158	0.95[CHB][hapmap]
rs380806	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs391304	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs394315	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs405449	0.83[AMR][1000 genomes]
rs432849	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438151	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs446760	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs472487	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs634680	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6483726	0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs360142	CNGA4	cis	parietal	SCAN
rs360142	PPFIBP2	cis	cerebellum	SCAN
rs360142	CSNK2A1P	cis	parietal	SCAN
rs360142	C11orf17	cis	parietal	SCAN
rs360142	MRPL17	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780200-9786600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
3	chr11:9780800-9786600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:9780800-9788600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:9780800-9788600	Enhancers	Fetal Heart	heart
6	chr11:9780800-9794200	Enhancers	Fetal Muscle Leg	muscle
7	chr11:9781000-9786800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:9781200-9789400	Enhancers	Placenta	Placenta
9	chr11:9781400-9786600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:9781400-9795200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:9781400-9800800	Weak transcription	Fetal Brain Female	brain
12	chr11:9781600-9786400	Weak transcription	Fetal Kidney	kidney
13	chr11:9781600-9786600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:9781600-9786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:9781600-9798200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr11:9781600-9801000	Weak transcription	Primary T cells from cord blood	blood
17	chr11:9781600-9809000	Weak transcription	Fetal Brain Male	brain
18	chr11:9781800-9786600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:9781800-9786600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:9781800-9790800	Enhancers	NHDF-Ad	bronchial
21	chr11:9781800-9799200	Weak transcription	Primary B cells from cord blood	blood
22	chr11:9781800-9799200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:9781800-9801200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:9781800-9801600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:9782000-9798000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:9782200-9786200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:9782200-9786600	Weak transcription	Fetal Intestine Large	intestine
28	chr11:9782200-9786600	Weak transcription	GM12878-XiMat	blood
29	chr11:9782200-9786800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:9782200-9786800	Weak transcription	Pancreas	Pancrea
31	chr11:9782200-9787000	Weak transcription	Lung	lung
32	chr11:9782200-9787000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:9782200-9787800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:9782200-9796200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:9782400-9786200	Weak transcription	HUVEC	blood vessel
36	chr11:9782400-9786600	Weak transcription	Fetal Intestine Small	intestine
37	chr11:9782400-9786600	Weak transcription	Hela-S3	cervix
38	chr11:9782400-9787000	Weak transcription	Colonic Mucosa	Colon
39	chr11:9782400-9791600	Weak transcription	A549	lung
40	chr11:9782400-9799400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:9782600-9786200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:9782600-9786200	Weak transcription	Adipose Nuclei	Adipose
43	chr11:9782600-9786200	Weak transcription	Fetal Stomach	stomach
44	chr11:9782600-9786200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:9782600-9786400	Weak transcription	Fetal Lung	lung
46	chr11:9782600-9786600	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:9782600-9786800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:9782600-9786800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:9782600-9787400	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:9782600-9797800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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