Variant report

Variant	rs12620018
Chromosome Location	chr2:73906408-73906409
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	chr2:73906056..73907836-chr2:74356105..74358909,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10190002	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs1052161	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs10865398	0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs11126413	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11126415	0.81[EUR][1000 genomes]
rs12052539	0.81[EUR][1000 genomes]
rs12053242	0.81[EUR][1000 genomes]
rs12618600	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs12620091	0.80[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12991161	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13007607	0.94[EUR][1000 genomes]
rs13017182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13018422	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13022145	0.93[EUR][1000 genomes]
rs13027816	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1320374	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs17350125	0.81[EUR][1000 genomes]
rs1806683	0.80[EUR][1000 genomes]
rs1815028	0.80[EUR][1000 genomes]
rs2017116	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs2421557	0.80[EUR][1000 genomes]
rs2421574	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2421581	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2421584	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421585	0.91[ASN][1000 genomes]
rs2421586	1.00[CEU][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421667	0.81[EUR][1000 genomes]
rs2421668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap]
rs2421669	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2948441	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs34874205	0.88[EUR][1000 genomes]
rs35421685	0.83[EUR][1000 genomes]
rs35498419	0.81[EUR][1000 genomes]
rs3820700	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs3980695	0.80[EUR][1000 genomes]
rs4241257	0.80[EUR][1000 genomes]
rs4341964	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4346412	0.80[EUR][1000 genomes]
rs4511748	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4637150	0.86[ASN][1000 genomes]
rs4852316	0.81[EUR][1000 genomes]
rs4852939	0.91[EUR][1000 genomes]
rs4852950	0.91[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4852954	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4852957	0.83[EUR][1000 genomes]
rs4852959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4852976	0.81[EUR][1000 genomes]
rs4852977	0.80[EUR][1000 genomes]
rs6546862	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6546865	0.82[ASN][1000 genomes]
rs6546870	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6712242	0.87[ASN][1000 genomes]
rs6722867	0.81[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs6742619	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6743576	0.81[EUR][1000 genomes]
rs6745560	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs6748233	0.80[EUR][1000 genomes]
rs6755948	0.88[EUR][1000 genomes]
rs7558546	0.81[EUR][1000 genomes]
rs7570683	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7574240	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574268	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7599323	0.83[CHB][hapmap]
rs7599453	0.81[EUR][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7609249	0.81[EUR][1000 genomes]
rs780390	0.92[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:48 , 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	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2760600	chr2:73846605-73911523	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv874271	chr2:73847024-73907696	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv874272	chr2:73847024-73914019	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv874273	chr2:73847024-73916672	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874274	chr2:73847024-73922475	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv874275	chr2:73847024-73931971	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	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
15	nsv1013586	chr2:73848777-73906844	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1004208	chr2:73849172-73911511	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv2497164	chr2:73850717-73912022	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1011488	chr2:73852525-73909818	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1000057	chr2:73852525-73911511	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv3385057	chr2:73853505-73913858	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv1013142	chr2:73854911-73911511	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1008311	chr2:73854911-73923089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv829460	chr2:73856145-73913711	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv582209	chr2:73857002-73907696	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv818044	chr2:73859184-73906819	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv515605	chr2:73859184-73916672	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	esv3334222	chr2:73867401-73923991	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv874277	chr2:73870010-73931971	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
29	nsv874278	chr2:73870010-73931971	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	esv3340115	chr2:73870416-73930142	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	nsv582210	chr2:73870573-73916672	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	nsv874279	chr2:73870573-73916672	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
33	nsv874280	chr2:73870573-73927764	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	esv2762675	chr2:73875799-73928886	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
35	nsv441760	chr2:73875799-73928886	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
36	esv3426494	chr2:73876125-73939153	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
37	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
38	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
39	nsv829461	chr2:73877427-73931225	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
40	nsv874281	chr2:73878352-73927764	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
41	nsv874282	chr2:73878827-73922475	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
42	nsv874283	chr2:73878827-73927764	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
43	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
44	nsv979022	chr2:73897805-73932073	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
45	nsv818046	chr2:73900329-73914019	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
46	nsv818047	chr2:73900329-73916672	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
47	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
48	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12620018	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs12620018	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs12620018	ALMS1P	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73900600-73912800	Weak transcription	Liver	Liver
2	chr2:73900600-73913000	Weak transcription	Pancreas	Pancrea
3	chr2:73900600-73954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:73901400-73913000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:73901600-73911400	Weak transcription	Ovary	ovary
6	chr2:73902200-73931400	Weak transcription	Brain Anterior Caudate	brain
7	chr2:73906200-73907000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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