Variant report

Variant	rs1052161
Chromosome Location	chr2:73828538-73828539
allele	C/T
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	chr2:73828531-73828550	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ALMS1	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10189578	0.85[EUR][1000 genomes]
rs10190002	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1083919	0.85[EUR][1000 genomes]
rs1083921	0.83[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1083923	0.84[EUR][1000 genomes]
rs10865398	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11126402	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11126413	0.80[EUR][1000 genomes]
rs11126414	0.81[TSI][hapmap]
rs11126417	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11688718	0.88[EUR][1000 genomes]
rs11894953	0.81[TSI][hapmap]
rs1246094	0.86[EUR][1000 genomes]
rs12618600	0.96[CEU][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs12620018	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs12620091	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs12713793	0.81[TSI][hapmap]
rs12713798	0.81[TSI][hapmap]
rs12991161	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12995433	0.81[EUR][1000 genomes]
rs12996463	0.82[EUR][1000 genomes]
rs13009035	0.95[EUR][1000 genomes]
rs13017182	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs13027816	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1320374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13386124	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13399087	0.87[EUR][1000 genomes]
rs1528169	0.82[EUR][1000 genomes]
rs17349804	0.80[ASN][1000 genomes]
rs17350188	0.81[TSI][hapmap]
rs1881246	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs1881247	0.85[JPT][hapmap]
rs2017116	0.87[JPT][hapmap]
rs2037814	0.87[JPT][hapmap]
rs2091504	0.83[EUR][1000 genomes]
rs2178154	0.85[EUR][1000 genomes]
rs2421545	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2421546	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2421548	0.82[EUR][1000 genomes]
rs2421574	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2421581	0.87[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2421583	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2421584	0.82[EUR][1000 genomes]
rs2421586	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs2421667	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421668	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs2421669	0.87[JPT][hapmap]
rs2421674	0.81[TSI][hapmap]
rs2421676	0.81[TSI][hapmap]
rs2948441	0.87[JPT][hapmap]
rs3820700	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs4346412	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4852305	0.81[JPT][hapmap]
rs4852308	0.95[EUR][1000 genomes]
rs4852927	0.80[EUR][1000 genomes]
rs4852936	0.95[ASN][1000 genomes]
rs4852939	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4852954	0.92[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs4852959	1.00[CEU][hapmap]
rs4852975	0.81[TSI][hapmap]
rs4852976	0.86[TSI][hapmap]
rs62153184	0.88[EUR][1000 genomes]
rs6546832	0.87[JPT][hapmap]
rs6546846	0.86[EUR][1000 genomes]
rs6546862	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6722867	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6723002	0.80[YRI][hapmap]
rs6729468	0.86[EUR][1000 genomes]
rs6730785	0.80[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6742619	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs6743576	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6744697	0.87[EUR][1000 genomes]
rs6745560	0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6746971	0.85[EUR][1000 genomes]
rs6749680	0.84[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs6755948	0.81[AMR][1000 genomes]
rs6757996	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7562047	0.86[EUR][1000 genomes]
rs7566315	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7570683	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs7574240	0.81[EUR][1000 genomes]
rs7574268	0.81[EUR][1000 genomes]
rs7585119	0.86[EUR][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7606483	0.83[EUR][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs7609249	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs780390	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs780391	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs780393	0.87[EUR][1000 genomes]
rs780394	0.84[EUR][1000 genomes]
rs780395	0.84[EUR][1000 genomes]
rs780396	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1052161	ALMS1	cis	parietal	SCAN
rs1052161	ALMS1P	cis	parietal	SCAN
rs1052161	DUSP11	cis	parietal	SCAN
rs1052161	DUSP11	cis	cerebellum	SCAN
rs1052161	MXD1	cis	cerebellum	SCAN
rs1052161	LRRTM4	cis	cerebellum	SCAN
rs1052161	CGI-121	cis	multi-tissue	Pritchard
rs1052161	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs1052161	MPHOSPH10	cis	cerebellum	SCAN
rs1052161	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1052161	ALMS1P	cis	cerebellum	SCAN
rs1052161	ALMS1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
2	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
3	chr2:73792200-73828600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:73800600-73828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:73800800-73828800	Weak transcription	HSMM	muscle
6	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
7	chr2:73807600-73829200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:73812800-73828600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:73815600-73836000	Weak transcription	A549	lung
10	chr2:73816000-73829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:73819600-73829400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:73821600-73830000	Weak transcription	Osteobl	bone
13	chr2:73821800-73830000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:73822000-73828600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
16	chr2:73822600-73833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:73823000-73830000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
20	chr2:73825400-73833600	Weak transcription	Esophagus	oesophagus
21	chr2:73826000-73832200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:73826200-73829200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:73826200-73833200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:73826600-73828600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:73826800-73828600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:73826800-73828800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:73826800-73829200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:73826800-73832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:73827000-73840600	Weak transcription	NHLF	lung
34	chr2:73827200-73831200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:73827200-73831600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:73827200-73837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:73827400-73830600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:73827400-73836400	Strong transcription	Primary T cells from cord blood	blood
39	chr2:73827600-73829200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr2:73827600-73830600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:73827600-73830600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:73827600-73831800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr2:73827600-73832400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:73827600-73837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:73827600-73838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:73827800-73829200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:73827800-73830000	Weak transcription	GM12878-XiMat	blood
49	chr2:73827800-73830400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:73827800-73830400	Strong transcription	Duodenum Mucosa	Duodenum

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