Variant report

Variant	rs2421559
Chromosome Location	chr2:73999654-73999655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73985050..73987926-chr2:73998150..74000912,3	MCF-7	breast:
2	chr2:73998796..74000757-chr2:74002407..74004456,2	MCF-7	breast:
3	chr2:73998583..74001137-chr2:74005182..74006875,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144048	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10172044	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10191988	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10193032	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs10203740	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208995	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11126414	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs11126415	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11126416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126417	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs11891140	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11892172	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12052539	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12053242	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12233112	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs12233115	0.83[AMR][1000 genomes]
rs12611487	0.81[AMR][1000 genomes]
rs12612423	0.80[AMR][1000 genomes]
rs12615807	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12619258	0.83[CEU][hapmap];0.89[AMR][1000 genomes]
rs12624267	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713789	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713790	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713791	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713793	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713794	0.87[EUR][1000 genomes]
rs12713795	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713797	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12992607	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12997568	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12998980	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs13003035	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13005729	0.86[AMR][1000 genomes]
rs13006448	0.86[AMR][1000 genomes]
rs13006598	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13013228	0.86[AMR][1000 genomes]
rs13014700	0.84[AMR][1000 genomes]
rs13015885	0.84[AMR][1000 genomes]
rs13017182	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs13020517	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13031853	0.86[AMR][1000 genomes]
rs13031866	0.87[AMR][1000 genomes]
rs13033744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13383097	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17350056	0.82[AMR][1000 genomes]
rs17350125	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17350188	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17434634	0.81[AMR][1000 genomes]
rs17434655	0.82[AMR][1000 genomes]
rs1806683	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1815028	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2001436	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs2001490	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs2006997	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2012574	0.87[AMR][1000 genomes]
rs2116367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272051	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272178	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421557	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421558	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2421574	0.92[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2421575	0.84[AMR][1000 genomes]
rs2421672	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421674	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421675	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421676	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2421677	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2462127	0.91[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35498419	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35767294	0.86[AMR][1000 genomes]
rs35791379	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3813228	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3980695	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4241257	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4358149	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4513320	0.83[AMR][1000 genomes]
rs4852316	0.85[EUR][1000 genomes]
rs4852972	0.81[AMR][1000 genomes]
rs4852975	0.83[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs4852976	0.87[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852977	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852978	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6732812	0.81[AMR][1000 genomes]
rs6745560	0.82[GIH][hapmap];0.87[MEX][hapmap]
rs6748233	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6749841	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6750494	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6750515	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6750877	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6755500	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7210	0.96[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs732778	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7368570	0.88[AMR][1000 genomes]
rs7370393	0.80[AMR][1000 genomes]
rs7558546	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7591112	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7597302	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7599453	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7606947	0.92[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs891695	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs891696	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9309475	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9309476	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	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
8	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2421559	ALMS1P	cis	parietal	SCAN
rs2421559	ALMS1	cis	cerebellum	SCAN
rs2421559	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2421559	DUSP11	cis	cerebellum	SCAN
rs2421559	ALMS1	cis	parietal	SCAN
rs2421559	ALMS1P	cis	Nerve Tibial	GTEx
rs2421559	DUSP11	cis	parietal	SCAN
rs2421559	TPRKB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr2:73971400-74002200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:73976600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:73977400-74001400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:73977400-74004800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:73977600-74004800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:73977800-74004000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:73978000-74004200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:73981600-74004800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr2:73982000-74004600	Strong transcription	Primary T cells from cord blood	blood
11	chr2:73982000-74004800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:73982000-74005200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:73982200-74002600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:73982200-74004000	Strong transcription	Dnd41	blood
15	chr2:73982200-74004800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:73982200-74005200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:73982400-74002400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:73982400-74002600	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr2:73982400-74004800	Strong transcription	Placenta	Placenta
20	chr2:73982400-74005000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:73982600-74005000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:73982600-74005000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:73982800-74004800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:73982800-74005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:73983000-74005000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:73983400-74004400	Strong transcription	HepG2	liver
27	chr2:73983600-74005400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:73983600-74006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:73983800-74006000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:73986200-74005200	Strong transcription	Fetal Thymus	thymus
31	chr2:73986600-74002400	Strong transcription	A549	lung
32	chr2:73986800-74001000	Strong transcription	GM12878-XiMat	blood
33	chr2:73986800-74002600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:73987000-74002600	Strong transcription	HSMM	muscle
35	chr2:73987000-74004400	Strong transcription	Hela-S3	cervix
36	chr2:73987000-74005200	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:73987200-74001600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:73987200-74005000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:73987200-74005400	Weak transcription	Psoas Muscle	Psoas
40	chr2:73987400-74002600	Strong transcription	Adipose Nuclei	Adipose
41	chr2:73987400-74004000	Strong transcription	NH-A	brain
42	chr2:73987400-74005000	Strong transcription	Liver	Liver
43	chr2:73987600-74002400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:73987600-74002400	Strong transcription	Fetal Lung	lung
45	chr2:73987600-74004000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:73987600-74004400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:73987600-74004400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:73987600-74004600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:73988200-74001800	Strong transcription	Left Ventricle	heart
50	chr2:73988200-74005400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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