Variant report

Variant	rs6745560
Chromosome Location	chr2:73827117-73827118
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	chr2:73825783..73827723-chr2:74425756..74427466,2	K562	blood:
2	chr2:73824033..73827858-chr2:73829276..73833224,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10189578	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10190002	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052161	0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs1083919	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1083921	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1083922	0.81[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1083923	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10865398	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11126402	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11126414	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs11688718	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11894953	0.87[MEX][hapmap]
rs12233112	0.93[YRI][hapmap]
rs1246094	0.82[EUR][1000 genomes]
rs12618600	0.92[CEU][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs12620018	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs12620091	0.84[CHD][hapmap]
rs12624267	0.82[GIH][hapmap]
rs12713793	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs12713798	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs12991161	0.96[CEU][hapmap]
rs12992607	0.93[YRI][hapmap]
rs13003035	0.93[YRI][hapmap]
rs13007607	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13009035	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13017182	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13018422	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13022145	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13027816	0.96[CEU][hapmap]
rs13033744	0.81[GIH][hapmap];0.83[MEX][hapmap]
rs1320374	0.83[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs13386124	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13399087	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1406105	0.93[CHD][hapmap]
rs1528169	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17350188	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs1852647	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs1881246	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1881247	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2017116	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2037814	0.84[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs2091503	0.83[AFR][1000 genomes]
rs2091504	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2178154	0.82[EUR][1000 genomes]
rs2272051	0.82[GIH][hapmap]
rs2421545	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2421546	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2421559	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs2421574	0.88[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2421581	0.87[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2421583	0.96[CEU][hapmap];0.93[JPT][hapmap]
rs2421586	0.96[CEU][hapmap];0.87[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs2421667	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421668	0.96[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs2421669	0.87[JPT][hapmap]
rs2421674	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs2421676	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs2948441	0.84[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs3813228	0.82[GIH][hapmap]
rs3820700	0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs4346412	0.94[EUR][1000 genomes]
rs4436991	0.86[ASN][1000 genomes]
rs4852305	0.81[JPT][hapmap]
rs4852306	0.84[AFR][1000 genomes]
rs4852308	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4852930	0.81[AFR][1000 genomes]
rs4852939	0.85[EUR][1000 genomes]
rs4852950	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4852951	0.96[CEU][hapmap]
rs4852954	0.88[CEU][hapmap];0.82[GIH][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap]
rs4852957	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4852959	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs4852975	0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs4852976	0.82[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap]
rs56054150	0.85[ASN][1000 genomes]
rs62153184	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6546832	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs6546846	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6722867	0.92[EUR][1000 genomes]
rs6729468	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6730785	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6732440	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6742619	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs6743576	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6744697	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6746971	0.82[EUR][1000 genomes]
rs6749680	1.00[ASW][hapmap];0.81[CEU][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6757996	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7210	0.82[GIH][hapmap]
rs7562047	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7566315	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570014	0.90[ASN][1000 genomes]
rs7570683	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs7585119	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7598660	0.92[CEU][hapmap];0.88[MEX][hapmap]
rs7598901	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7599323	0.83[CHD][hapmap]
rs7606483	0.85[EUR][1000 genomes]
rs7606947	0.88[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs7609034	0.89[ASN][1000 genomes]
rs7609249	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780390	0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs780391	0.84[EUR][1000 genomes]
rs780393	0.83[EUR][1000 genomes]
rs780394	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs780395	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs780396	0.84[CHB][hapmap];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6745560	ALMS1P	cis	Whole Blood	GTEx
rs6745560	ALMS1P	cis	Nerve Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
2	chr2:73760600-73828000	Weak transcription	Right Ventricle	heart
3	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
4	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
5	chr2:73792200-73828600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:73797400-73828400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:73800400-73827600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:73800600-73828000	Weak transcription	Gastric	stomach
9	chr2:73800600-73828400	Weak transcription	Aorta	Aorta
10	chr2:73800600-73828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:73800800-73827800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:73800800-73827800	Weak transcription	Left Ventricle	heart
13	chr2:73800800-73828000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:73800800-73828200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:73800800-73828800	Weak transcription	HSMM	muscle
16	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
17	chr2:73807000-73828200	Weak transcription	Fetal Thymus	thymus
18	chr2:73807600-73828000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:73807600-73828000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:73807600-73829200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:73807800-73827400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:73808200-73827800	Weak transcription	Fetal Stomach	stomach
23	chr2:73808400-73828000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:73808600-73828000	Weak transcription	Thymus	Thymus
25	chr2:73808800-73828000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:73808800-73828000	Weak transcription	Adipose Nuclei	Adipose
27	chr2:73812800-73828600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:73815600-73827400	Weak transcription	Primary T cells from cord blood	blood
29	chr2:73815600-73827600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:73815600-73828200	Weak transcription	Fetal Brain Female	brain
31	chr2:73815600-73828200	Weak transcription	HepG2	liver
32	chr2:73815600-73828400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:73815600-73828400	Weak transcription	Brain Anterior Caudate	brain
34	chr2:73815600-73836000	Weak transcription	A549	lung
35	chr2:73815800-73828000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:73815800-73828200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:73816000-73827800	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:73816000-73828000	Weak transcription	Brain Angular Gyrus	brain
39	chr2:73816000-73829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:73816400-73827800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:73817400-73827800	Weak transcription	Fetal Intestine Large	intestine
42	chr2:73819600-73829400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:73820000-73828000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:73820600-73828400	Weak transcription	Spleen	Spleen
45	chr2:73821000-73828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:73821400-73828000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:73821600-73830000	Weak transcription	Osteobl	bone
48	chr2:73821800-73828200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:73821800-73828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:73821800-73830000	Weak transcription	Muscle Satellite Cultured Cells	--

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