Variant report

Variant	rs2272178
Chromosome Location	chr2:73977609-73977610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DUSP11-2	chr2:73977383-73977913	ENSG00000273245.1

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10172044	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10191988	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10193032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10203740	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10208995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126414	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11126415	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11126416	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11126417	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11891140	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11892172	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11894953	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12052539	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12053242	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12233112	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12233115	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12611487	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12612423	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12615807	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12619258	0.88[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12624267	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713788	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12713789	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713790	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713791	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713794	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12713795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713797	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713798	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12992607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12997568	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12998980	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13000788	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13003035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005729	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13006448	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13006598	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13013228	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13014700	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13015885	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13020517	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13031853	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13031866	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13033744	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13383097	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17009372	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs17350056	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17350125	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17350188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17434634	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17434655	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1806683	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1815028	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2001436	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2001490	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2006997	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2012574	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2116367	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2272051	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2421557	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421558	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421559	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421575	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2421672	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2421676	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421677	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2462127	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35498419	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35767294	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35791379	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3813228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3980695	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4241257	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4358149	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4513320	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4530394	0.84[EUR][1000 genomes]
rs4852316	0.89[EUR][1000 genomes]
rs4852972	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4852975	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4852976	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4852977	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4852978	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6732812	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6748233	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6749841	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6750494	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6750515	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6750877	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755500	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs732778	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7368570	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7370393	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7558546	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7591112	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7597302	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7599453	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs891695	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs891696	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309475	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309476	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2272178	ALMS1P	cis	Nerve Tibial	GTEx
rs2272178	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2272178	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr2:73965000-73978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:73965000-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:73965400-73982200	Weak transcription	Hela-S3	cervix
5	chr2:73965400-73985600	Weak transcription	Fetal Heart	heart
6	chr2:73965400-73986200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:73965400-73986600	Weak transcription	Psoas Muscle	Psoas
8	chr2:73966200-73992000	Weak transcription	Stomach Mucosa	stomach
9	chr2:73967600-73978800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:73969400-73983400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:73969400-73987200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:73969600-73986000	Weak transcription	Right Ventricle	heart
13	chr2:73969800-73982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:73969800-73982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:73970400-73981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:73971400-74002200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:73971600-73987000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:73972000-73978800	Weak transcription	Brain Anterior Caudate	brain
19	chr2:73972000-73992200	Weak transcription	Fetal Kidney	kidney
20	chr2:73973200-73980800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:73973200-73980800	Strong transcription	GM12878-XiMat	blood
22	chr2:73973400-73982200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:73973400-73987400	Weak transcription	Colonic Mucosa	Colon
24	chr2:73973600-73978200	Weak transcription	HepG2	liver
25	chr2:73973800-73978000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:73973800-73978000	Weak transcription	Gastric	stomach
27	chr2:73973800-73978400	Weak transcription	Dnd41	blood
28	chr2:73973800-73979000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:73973800-73979600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:73973800-73981000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:73973800-73982200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:73974000-73977800	Weak transcription	Ovary	ovary
33	chr2:73974000-73978400	Weak transcription	Fetal Brain Female	brain
34	chr2:73974000-73978800	Weak transcription	Brain Angular Gyrus	brain
35	chr2:73974000-73979000	Weak transcription	Spleen	Spleen
36	chr2:73974000-73979200	Weak transcription	Fetal Lung	lung
37	chr2:73974000-73979200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:73974000-73979800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:73974000-73983400	Weak transcription	Pancreas	Pancrea
40	chr2:73974000-73984800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:73974000-73984800	Weak transcription	Esophagus	oesophagus
42	chr2:73974000-73986000	Weak transcription	Small Intestine	intestine
43	chr2:73974000-73989000	Weak transcription	Fetal Brain Male	brain
44	chr2:73974200-73977800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:73974200-73978800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:73974200-73978800	Weak transcription	Left Ventricle	heart
47	chr2:73974200-73979000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:73974200-73979400	Weak transcription	K562	blood
49	chr2:73974200-73979600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:73974200-73982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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