Variant report

Variant	rs12991161
Chromosome Location	chr2:73871371-73871372
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73868945..73872912-chr2:73927731..73932752,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204872	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10190002	1.00[CEU][hapmap]
rs1052161	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap]
rs10865398	0.96[CEU][hapmap]
rs11126407	0.96[ASN][1000 genomes]
rs11126408	0.96[ASN][1000 genomes]
rs11126409	0.96[ASN][1000 genomes]
rs11126411	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11126413	0.95[EUR][1000 genomes]
rs11680056	0.90[ASN][1000 genomes]
rs11689234	0.88[CHB][hapmap]
rs12151671	0.96[ASN][1000 genomes]
rs12478871	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs12618600	0.96[CEU][hapmap]
rs12620018	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12620091	0.80[CEU][hapmap]
rs12620569	0.96[ASN][1000 genomes]
rs13007607	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13007623	0.96[ASN][1000 genomes]
rs13017182	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13018422	0.94[EUR][1000 genomes]
rs13022145	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320374	1.00[CEU][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs1879662	0.97[ASN][1000 genomes]
rs1879666	0.96[ASN][1000 genomes]
rs2280506	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2280507	1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs2421574	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2421582	0.95[CEU][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2421583	1.00[CEU][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2421584	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421587	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2421589	0.94[ASN][1000 genomes]
rs2421590	0.96[ASN][1000 genomes]
rs2421591	0.96[ASN][1000 genomes]
rs2421667	0.81[EUR][1000 genomes]
rs2421668	1.00[CEU][hapmap]
rs28708576	0.95[ASN][1000 genomes]
rs2947845	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs34719281	0.96[ASN][1000 genomes]
rs34874205	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35421685	0.82[EUR][1000 genomes]
rs3980696	0.90[ASN][1000 genomes]
rs4341964	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4346412	0.80[EUR][1000 genomes]
rs4443018	0.97[ASN][1000 genomes]
rs4444558	0.82[ASN][1000 genomes]
rs4627598	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4852310	0.96[ASN][1000 genomes]
rs4852311	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4852939	0.91[EUR][1000 genomes]
rs4852948	0.95[ASN][1000 genomes]
rs4852949	0.96[ASN][1000 genomes]
rs4852950	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4852951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852953	0.86[ASN][1000 genomes]
rs4852954	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4852956	0.96[ASN][1000 genomes]
rs4852957	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4852958	0.94[ASN][1000 genomes]
rs4852959	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4852974	0.81[CHB][hapmap]
rs6546862	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546863	0.96[ASN][1000 genomes]
rs6718799	0.96[ASN][1000 genomes]
rs6722867	0.81[EUR][1000 genomes]
rs6725284	0.95[ASN][1000 genomes]
rs6729347	0.96[ASN][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.84[YRI][hapmap];0.80[EUR][1000 genomes]
rs6742619	0.92[CEU][hapmap]
rs6743576	0.81[EUR][1000 genomes]
rs6744273	0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6745560	0.96[CEU][hapmap]
rs6749680	0.84[CEU][hapmap]
rs6755948	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72811975	0.91[ASN][1000 genomes]
rs7570683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574240	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7574268	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7579068	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7585668	0.96[ASN][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap]
rs7606947	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7607989	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7609249	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:38 , 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	nsv1015036	chr2:73840055-73891004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1006235	chr2:73840055-73896603	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1006033	chr2:73840055-73900856	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv979021	chr2:73847283-73871861	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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
22	nsv1004886	chr2:73852525-73900856	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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
34	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
35	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
36	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
37	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
38	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12991161	ALMS1P	cis	Nerve Tibial	GTEx
rs12991161	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs12991161	TPRKB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73867000-73872200	Enhancers	Ovary	ovary
2	chr2:73867600-73872200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:73868400-73871400	Enhancers	Primary hematopoietic stem cells	blood
4	chr2:73868600-73877000	Weak transcription	Gastric	stomach
5	chr2:73869600-73872000	Enhancers	Lung	lung
6	chr2:73870000-73872200	Weak transcription	Left Ventricle	heart
7	chr2:73870200-73871600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:73870200-73872200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:73870200-73874600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:73870400-73871800	Enhancers	HepG2	liver
11	chr2:73870600-73873800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:73871000-73871400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:73871000-73871400	Enhancers	Placenta	Placenta
14	chr2:73871000-73872200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr2:73871200-73871400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr2:73871200-73871800	Weak transcription	Spleen	Spleen
17	chr2:73871200-73878800	Weak transcription	Liver	Liver

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