Variant report

Variant	rs12283177
Chromosome Location	chr11:71215483-71215484
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71212078..71213595-chr11:71215421..71217314,2	K562	blood:
2	chr11:71214959..71216939-chr11:71218643..71221307,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KRTAP5-7-1	chr11:71214910-71216920	NONHSAT022690
2	lnc-KRTAP5-7-1	chr11:71215112-71215524	NONHSAT022689

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1002171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160376	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10160536	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11233868	0.86[EUR][1000 genomes]
rs11233947	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234008	0.86[YRI][hapmap]
rs11501814	0.90[EUR][1000 genomes]
rs12273154	0.86[EUR][1000 genomes]
rs12275121	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12275635	0.86[EUR][1000 genomes]
rs12275636	0.86[EUR][1000 genomes]
rs12277408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12277617	0.88[YRI][hapmap]
rs12283114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286569	0.88[EUR][1000 genomes]
rs12286616	0.88[EUR][1000 genomes]
rs12288906	0.86[EUR][1000 genomes]
rs12289036	0.96[EUR][1000 genomes]
rs12289074	0.96[EUR][1000 genomes]
rs12289358	0.81[EUR][1000 genomes]
rs12291219	0.86[YRI][hapmap]
rs12293132	0.86[YRI][hapmap]
rs12574206	0.86[EUR][1000 genomes]
rs12574554	0.86[EUR][1000 genomes]
rs12575605	0.86[EUR][1000 genomes]
rs12575622	0.90[EUR][1000 genomes]
rs12576621	0.86[EUR][1000 genomes]
rs12577807	0.90[EUR][1000 genomes]
rs17161576	0.94[EUR][1000 genomes]
rs17161578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893058	0.86[EUR][1000 genomes]
rs2298775	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2298776	0.90[EUR][1000 genomes]
rs28722015	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28823295	0.86[EUR][1000 genomes]
rs28898287	0.86[EUR][1000 genomes]
rs3794061	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3794062	0.86[EUR][1000 genomes]
rs3794064	0.86[EUR][1000 genomes]
rs3794068	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3814732	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3814733	0.86[EUR][1000 genomes]
rs57017893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57197278	0.86[EUR][1000 genomes]
rs57500217	0.86[EUR][1000 genomes]
rs57557229	0.86[EUR][1000 genomes]
rs57718633	0.92[EUR][1000 genomes]
rs58615796	0.90[EUR][1000 genomes]
rs59379414	0.86[EUR][1000 genomes]
rs59422671	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59487812	0.86[EUR][1000 genomes]
rs59511885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59972361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114525	0.86[EUR][1000 genomes]
rs7120978	0.86[EUR][1000 genomes]
rs7121106	0.86[EUR][1000 genomes]
rs7129044	0.86[EUR][1000 genomes]
rs7130479	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7483469	0.84[EUR][1000 genomes]
rs753352	0.84[EUR][1000 genomes]
rs7940351	0.92[EUR][1000 genomes]
rs7943296	0.85[EUR][1000 genomes]
rs7950649	0.89[JPT][hapmap];0.86[YRI][hapmap]
rs7952035	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv468632	chr11:71200320-71289089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv555402	chr11:71200320-71289089	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv3471041	chr11:71212614-71215837	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3471052	chr11:71212614-71215837	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv20567	chr11:71212774-71215694	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12283177	NADSYN1	cis	Artery Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:71181400-71217800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr11:71181800-71218000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:71182000-71217600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
9	chr11:71182400-71217200	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:71182400-71217600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:71182400-71217800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr11:71182800-71216400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr11:71189800-71218400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:71199400-71215600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:71199600-71216400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:71199600-71218400	Strong transcription	Fetal Intestine Small	intestine
17	chr11:71200000-71216000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:71200200-71216000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:71200200-71216400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:71200200-71217400	Strong transcription	Fetal Intestine Large	intestine
21	chr11:71200400-71216200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:71200400-71216400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr11:71200800-71216800	Weak transcription	Fetal Kidney	kidney
24	chr11:71201000-71216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:71201800-71216400	Strong transcription	Ovary	ovary
26	chr11:71203400-71216800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:71205200-71215600	Strong transcription	Colonic Mucosa	Colon
28	chr11:71205200-71215600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:71205200-71216000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:71207200-71215800	Strong transcription	Pancreas	Pancrea
31	chr11:71207800-71215800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:71209400-71218800	Weak transcription	Small Intestine	intestine
33	chr11:71210200-71217600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr11:71210400-71216000	Strong transcription	Dnd41	blood
35	chr11:71210400-71217800	Weak transcription	Osteobl	bone
36	chr11:71210400-71220200	Weak transcription	NHEK	skin
37	chr11:71210600-71219200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:71210800-71215800	Strong transcription	Thymus	Thymus
39	chr11:71211600-71218800	Weak transcription	HMEC	breast
40	chr11:71211800-71216200	Weak transcription	Stomach Mucosa	stomach
41	chr11:71211800-71217400	Strong transcription	Gastric	stomach
42	chr11:71211800-71220600	Weak transcription	NH-A	brain
43	chr11:71211800-71232400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:71212000-71215800	Strong transcription	Spleen	Spleen
45	chr11:71212000-71215800	Weak transcription	A549	lung
46	chr11:71212000-71216200	Weak transcription	Fetal Lung	lung
47	chr11:71212000-71218200	Weak transcription	HSMMtube	muscle
48	chr11:71212000-71220600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr11:71212200-71215600	Weak transcription	HUVEC	blood vessel
50	chr11:71212200-71216200	Strong transcription	Adipose Nuclei	Adipose

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