Variant report

Variant	rs3980695
Chromosome Location	chr2:73939552-73939553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73934847..73936533-chr2:73939356..73942331,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10172044	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10191988	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10200762	0.86[EUR][1000 genomes]
rs10203740	0.83[EUR][1000 genomes]
rs10208995	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11126413	0.81[EUR][1000 genomes]
rs11126414	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11126415	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11126416	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11126417	0.90[EUR][1000 genomes]
rs11891140	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11892172	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11894953	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12052539	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12053242	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12233112	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12233115	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12611487	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12612423	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12615807	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619258	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12620018	0.80[EUR][1000 genomes]
rs12624267	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713788	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713789	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713790	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713791	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713793	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713794	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713795	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713797	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713798	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12992607	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12997568	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12998980	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13000788	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13003035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13005729	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13006448	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13006598	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13013228	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13014700	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13015885	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13020517	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13022837	0.81[AMR][1000 genomes]
rs13026192	0.85[EUR][1000 genomes]
rs13027816	0.81[EUR][1000 genomes]
rs13031853	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13031866	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13033744	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13383097	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17350056	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17350125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17350188	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17434634	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17434655	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1806683	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001436	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001490	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2006997	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2012574	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2116367	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2272051	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2272178	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421558	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421559	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421574	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2421575	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421582	0.81[EUR][1000 genomes]
rs2421583	0.81[EUR][1000 genomes]
rs2421584	0.81[EUR][1000 genomes]
rs2421586	0.81[EUR][1000 genomes]
rs2421672	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421674	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421676	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421677	0.91[EUR][1000 genomes]
rs2462127	0.83[EUR][1000 genomes]
rs35421685	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35498419	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35528262	0.80[EUR][1000 genomes]
rs35767294	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35791379	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3813228	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4241257	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4358149	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4513320	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4530394	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4852316	0.98[EUR][1000 genomes]
rs4852959	0.81[EUR][1000 genomes]
rs4852966	0.81[EUR][1000 genomes]
rs4852972	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4852975	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4852976	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4852977	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4852978	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732812	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6748233	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749841	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6750494	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6750515	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6750877	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6755500	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7210	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs732778	0.83[EUR][1000 genomes]
rs7368570	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7370393	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7558546	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7570683	0.81[EUR][1000 genomes]
rs7574240	0.82[EUR][1000 genomes]
rs7574268	0.82[EUR][1000 genomes]
rs7591112	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7597302	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7599453	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7606947	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7608328	0.82[ASN][1000 genomes]
rs891695	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs891696	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9309475	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9309476	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv3460808	chr2:73877074-73940302	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3460809	chr2:73877074-73940302	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv2753082	chr2:73891045-73955545	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv34157	chr2:73901718-73949151	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv1003153	chr2:73927235-73975416	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	esv3366619	chr2:73932602-73946742	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3980695	ALMS1P	cis	Nerve Tibial	GTEx
rs3980695	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs3980695	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73900600-73954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:73927800-73954800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:73932200-73943400	Weak transcription	Ovary	ovary
4	chr2:73935000-73955200	Weak transcription	Colonic Mucosa	Colon
5	chr2:73936400-73943400	Weak transcription	Fetal Intestine Large	intestine

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