Variant report

Variant	rs1790324
Chromosome Location	chr11:71150520-71150521
allele	A/C
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	POLR2A	chr11:71150155-71150659	K562	blood:	n/a	n/a
2	POLR2A	chr11:71147942-71151728	K562	blood:	n/a	n/a
3	POLR2A	chr11:71150511-71150709	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
DHCR7	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10898144	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11603330	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs11606033	0.81[CEU][hapmap]
rs12224205	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12419279	1.00[CEU][hapmap]
rs12419334	0.84[TSI][hapmap]
rs12422045	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs12797951	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1540127	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1619577	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1629220	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1630498	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790328	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790330	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790339	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790340	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1790341	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790343	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790344	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790345	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790350	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790353	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792224	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792226	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792227	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792229	0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792231	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792233	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792234	0.94[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792235	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792264	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792277	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792280	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1792281	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792282	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1792283	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1792284	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792315	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894100	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2002064	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2017686	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276358	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276362	0.80[CEU][hapmap]
rs2282621	0.82[TSI][hapmap]
rs2511010	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3750997	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs3794057	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4402322	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4435028	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4616066	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944957	0.82[TSI][hapmap]
rs736894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928249	0.82[TSI][hapmap]
rs7935125	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	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
7	nsv518163	chr11:71142350-71155153	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv933564	chr11:71148635-71152521	Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1790324	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs1790324	NADSYN1	cis	lymphoblastoid	seeQTL
rs1790324	RAB6A	cis	cerebellum	SCAN
rs1790324	AIP	cis	parietal	SCAN
rs1790324	RP11-660L16.2	cis	Thyroid	GTEx
rs1790324	NADSYN1	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71135000-71150600	Weak transcription	NH-A	brain
2	chr11:71140600-71158200	Weak transcription	Fetal Brain Male	brain
3	chr11:71140800-71154000	Weak transcription	Fetal Lung	lung
4	chr11:71140800-71154000	Weak transcription	HSMM	muscle
5	chr11:71143000-71150600	Weak transcription	Osteobl	bone
6	chr11:71144000-71156200	Strong transcription	Fetal Brain Female	brain
7	chr11:71144200-71152000	Weak transcription	Fetal Thymus	thymus
8	chr11:71144200-71158200	Weak transcription	Small Intestine	intestine
9	chr11:71144400-71156200	Strong transcription	Primary T cells from cord blood	blood
10	chr11:71144600-71157800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:71144800-71156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:71144800-71156800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:71144800-71156800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:71144800-71157800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr11:71145000-71150800	Weak transcription	A549	lung
16	chr11:71145000-71155400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:71145000-71156400	Strong transcription	Brain Germinal Matrix	brain
18	chr11:71145000-71156600	Strong transcription	Fetal Stomach	stomach
19	chr11:71145000-71157000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:71145000-71157000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:71145000-71157400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:71145000-71157800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:71145000-71158600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:71145200-71156200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr11:71145200-71157000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:71145200-71157000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:71145200-71157200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:71145200-71157400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:71145200-71157400	Strong transcription	HMEC	breast
30	chr11:71145200-71157800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr11:71145400-71157800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:71145400-71158000	Weak transcription	Stomach Mucosa	stomach
33	chr11:71145600-71157000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:71145600-71157000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:71145600-71158000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:71145800-71155400	Strong transcription	Left Ventricle	heart
37	chr11:71145800-71156200	Strong transcription	Lung	lung
38	chr11:71145800-71156400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:71145800-71156600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:71145800-71156600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:71145800-71156800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr11:71145800-71156800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr11:71145800-71157000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr11:71145800-71157200	Strong transcription	HSMMtube	muscle
45	chr11:71145800-71157400	Strong transcription	Fetal Intestine Large	intestine
46	chr11:71145800-71157800	Strong transcription	Fetal Intestine Small	intestine
47	chr11:71146000-71153800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr11:71146000-71155800	Strong transcription	HepG2	liver
49	chr11:71146000-71156200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:71146000-71156800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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