Variant report

Variant	rs10190002
Chromosome Location	chr2:73794054-73794055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73788145..73790335-chr2:73793829..73795838,2	MCF-7	breast:
2	chr2:73793527..73795637-chr2:73799230..73800827,2	MCF-7	breast:
3	chr14:24582941..24583875-chr2:73793545..73794452,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100897	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10189578	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10198549	0.82[YRI][hapmap]
rs1052161	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	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1083921	0.88[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1083923	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1091568	0.83[ASN][1000 genomes]
rs11126399	1.00[CHB][hapmap]
rs11126402	0.95[EUR][1000 genomes]
rs11126414	0.81[TSI][hapmap]
rs11126417	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs11685372	0.90[ASN][1000 genomes]
rs11688718	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11689767	0.88[ASN][1000 genomes]
rs11890811	0.81[LWK][hapmap]
rs11894953	0.81[TSI][hapmap]
rs1246094	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs12618600	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs12620018	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs12620091	0.82[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap]
rs12713793	0.81[TSI][hapmap]
rs12713798	0.81[TSI][hapmap]
rs12991161	1.00[CEU][hapmap]
rs12995433	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12996463	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13009035	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13017182	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap]
rs13027816	1.00[CEU][hapmap]
rs1320374	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs13386124	0.94[EUR][1000 genomes]
rs13398956	0.82[YRI][hapmap]
rs13399087	0.93[EUR][1000 genomes]
rs1403412	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs1406105	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs1528169	0.87[EUR][1000 genomes]
rs17350188	0.81[TSI][hapmap]
rs1852647	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1881246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2037814	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2091503	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2091504	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2140194	0.81[YRI][hapmap]
rs2178154	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs2421548	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421574	0.92[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs2421581	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2421583	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2421586	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs2421667	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421668	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs2421669	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2421674	0.81[TSI][hapmap]
rs2421676	0.81[TSI][hapmap]
rs2948441	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs3820700	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs4346412	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4511748	0.92[CHB][hapmap]
rs4852305	0.87[JPT][hapmap]
rs4852306	0.81[EUR][1000 genomes]
rs4852308	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4852927	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4852939	0.84[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap]
rs4852954	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs4852959	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs4852975	0.81[TSI][hapmap]
rs4852976	0.86[TSI][hapmap]
rs55677218	0.90[ASN][1000 genomes]
rs56054150	0.90[ASN][1000 genomes]
rs56068325	0.95[ASN][1000 genomes]
rs56770679	0.83[ASN][1000 genomes]
rs62153184	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6546826	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs6546827	0.92[CHB][hapmap]
rs6546829	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6546832	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6546842	0.87[ASN][1000 genomes]
rs6546846	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6546870	0.92[CHB][hapmap]
rs66931335	0.92[ASN][1000 genomes]
rs6706235	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs6710659	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6711285	0.85[YRI][hapmap]
rs6722867	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6723002	0.89[YRI][hapmap]
rs6729468	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6730785	0.85[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6742619	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6743576	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6744697	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6745560	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]
rs6746971	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs6749680	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6757996	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67877078	0.96[ASN][1000 genomes]
rs67898050	0.87[ASN][1000 genomes]
rs68154245	0.88[ASN][1000 genomes]
rs72811933	0.80[ASN][1000 genomes]
rs72811939	0.91[ASN][1000 genomes]
rs7562047	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7566315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570683	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs7571147	0.81[YRI][hapmap]
rs7574291	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs7576824	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs7585119	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7594511	0.85[YRI][hapmap]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7606483	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs7608308	0.96[ASN][1000 genomes]
rs7609249	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs780388	0.85[ASN][1000 genomes]
rs780389	0.85[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs780391	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs780393	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs780394	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs780395	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs802113	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10190002	MXD1	cis	cerebellum	SCAN
rs10190002	ALMS1	cis	brain	seeQTL
rs10190002	DUSP11	cis	parietal	SCAN
rs10190002	ALMS1	cis	parietal	SCAN
rs10190002	DUSP11	cis	cerebellum	SCAN
rs10190002	MPHOSPH10	cis	cerebellum	SCAN
rs10190002	ALMS1	cis	cerebellum	SCAN
rs10190002	ALMS1	trans	brain	seeQTL
rs10190002	ALMS1P	cis	cerebellum	SCAN
rs10190002	CGI-121	cis	multi-tissue	Pritchard
rs10190002	LRRTM4	cis	cerebellum	SCAN
rs10190002	ALMS1P	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
2	chr2:73744200-73799800	Weak transcription	NH-A	brain
3	chr2:73758000-73799800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:73758200-73800200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
6	chr2:73760600-73828000	Weak transcription	Right Ventricle	heart
7	chr2:73764600-73806800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:73764600-73807200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:73765200-73807800	Weak transcription	Brain Anterior Caudate	brain
10	chr2:73765400-73808400	Weak transcription	HepG2	liver
11	chr2:73765600-73799600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:73765800-73815400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
14	chr2:73766000-73807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:73766400-73799400	Weak transcription	Thymus	Thymus
16	chr2:73766400-73799600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:73766400-73799600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:73766400-73799600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:73766400-73799600	Weak transcription	Lung	lung
20	chr2:73766400-73803200	Weak transcription	Fetal Intestine Large	intestine
21	chr2:73769200-73802800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:73772000-73799600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:73772200-73799400	Weak transcription	Fetal Brain Female	brain
24	chr2:73773200-73795200	Weak transcription	Small Intestine	intestine
25	chr2:73775600-73811400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:73776000-73799600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:73776000-73801200	Weak transcription	GM12878-XiMat	blood
28	chr2:73776000-73821600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:73776400-73807800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:73778600-73799800	Weak transcription	Fetal Stomach	stomach
31	chr2:73778600-73811400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:73778800-73806200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:73779800-73799400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:73779800-73799800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:73780600-73796800	Weak transcription	HUVEC	blood vessel
36	chr2:73782200-73811400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:73782600-73808000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:73783600-73799800	Weak transcription	Primary B cells from cord blood	blood
39	chr2:73784200-73808200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:73784400-73799600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr2:73784400-73799800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:73785200-73815400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
44	chr2:73785600-73799800	Weak transcription	Left Ventricle	heart
45	chr2:73786000-73800200	Weak transcription	HMEC	breast
46	chr2:73786200-73799400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:73786200-73815400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:73786400-73799400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:73786400-73799600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:73786400-73800400	Weak transcription	Brain Substantia Nigra	brain

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