Variant report

Variant	rs35791379
Chromosome Location	chr2:73979482-73979483
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	POLR2A	chr2:73979366-73979515	K562	blood:	n/a	n/a
2	POLR2A	chr2:73979376-73979574	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000273245	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10172044	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191988	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10193032	0.81[CHB][hapmap];0.80[CHD][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs10203740	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10208995	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11126414	0.87[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11126415	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11126416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126417	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs11891140	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11892172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11894953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12052539	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12053242	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12233112	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12233115	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12611487	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12612423	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12615807	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12619258	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12624267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713788	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713789	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713790	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713791	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12713793	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713794	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713795	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713797	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12992607	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12997568	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12998980	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13000788	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13003035	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13005729	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13006448	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13006598	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13013228	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13014700	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13015885	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13017182	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs13020517	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13031853	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13031866	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13033744	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13383097	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17350056	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17350125	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17350188	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17434634	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17434655	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1806683	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1815028	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2001436	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2001490	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2006997	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2012574	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2116367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272051	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272178	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421557	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2421558	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2421559	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421574	0.92[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2421575	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2421672	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2421674	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2421675	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421677	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462127	0.88[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35498419	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35767294	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3813228	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3980695	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4241257	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4358149	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4513320	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4530394	0.83[EUR][1000 genomes]
rs4852316	0.88[EUR][1000 genomes]
rs4852972	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4852975	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4852976	0.91[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4852977	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4852978	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6732812	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6745560	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs6748233	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6749841	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6750494	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6750515	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6750877	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6755500	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7210	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs732778	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7368570	0.90[AMR][1000 genomes]
rs7370393	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7558546	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7591112	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7597302	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7599453	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7606947	0.92[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs891695	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs891696	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9309475	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309476	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv998315	chr2:73919185-74003998	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs35791379	ALMS1P	cis	Nerve Tibial	GTEx
rs35791379	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs35791379	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs35791379	DUSP11	cis	cerebellum	SCAN
rs35791379	ALMS1	cis	parietal	SCAN
rs35791379	ALMS1	cis	cerebellum	SCAN
rs35791379	DUSP11	cis	parietal	SCAN
rs35791379	ALMS1P	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73964600-74005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:73965000-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:73965400-73982200	Weak transcription	Hela-S3	cervix
4	chr2:73965400-73985600	Weak transcription	Fetal Heart	heart
5	chr2:73965400-73986200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:73965400-73986600	Weak transcription	Psoas Muscle	Psoas
7	chr2:73966200-73992000	Weak transcription	Stomach Mucosa	stomach
8	chr2:73969400-73983400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:73969400-73987200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:73969600-73986000	Weak transcription	Right Ventricle	heart
11	chr2:73969800-73982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:73969800-73982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:73970400-73981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:73971400-74002200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:73971600-73987000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:73972000-73992200	Weak transcription	Fetal Kidney	kidney
17	chr2:73973200-73980800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:73973200-73980800	Strong transcription	GM12878-XiMat	blood
19	chr2:73973400-73982200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:73973400-73987400	Weak transcription	Colonic Mucosa	Colon
21	chr2:73973800-73979600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:73973800-73981000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:73973800-73982200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:73974000-73979800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:73974000-73983400	Weak transcription	Pancreas	Pancrea
26	chr2:73974000-73984800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:73974000-73984800	Weak transcription	Esophagus	oesophagus
28	chr2:73974000-73986000	Weak transcription	Small Intestine	intestine
29	chr2:73974000-73989000	Weak transcription	Fetal Brain Male	brain
30	chr2:73974200-73979600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:73974200-73982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:73974200-73984600	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:73974200-73986800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:73974400-73979600	Weak transcription	NHLF	lung
35	chr2:73974400-73982200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:73974400-73987000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:73974600-73985800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:73975400-73981800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:73976400-73986200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:73976600-73980600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:73976600-73981000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:73976600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:73976800-73980800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:73976800-73981000	Strong transcription	Fetal Stomach	stomach
45	chr2:73977000-73980600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:73977000-73980600	Strong transcription	Lung	lung
47	chr2:73977000-73980800	Strong transcription	A549	lung
48	chr2:73977000-73981000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:73977000-73981200	Strong transcription	Fetal Intestine Small	intestine
50	chr2:73977000-73984000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links