Variant report

Variant	rs12998980
Chromosome Location	chr2:73930726-73930727
allele	A/C
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:
2	chr2:73920861..73923082-chr2:73929614..73932212,2	K562	blood:

Variant related genes	Relation type
ENSG00000144035	Chromatin interaction
ENSG00000163016	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10172044	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10191988	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10200762	0.92[EUR][1000 genomes]
rs10208995	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11126414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126415	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11126416	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11126417	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11689234	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11891140	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11892172	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs11894953	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052539	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12053242	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12233112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233115	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478871	0.92[CHB][hapmap]
rs12611487	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12612423	0.83[AMR][1000 genomes]
rs12615807	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12619258	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12624267	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12713788	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12713789	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713790	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713791	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713793	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12713794	0.83[EUR][1000 genomes]
rs12713795	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12713797	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12713798	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12992607	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12997018	0.85[EUR][1000 genomes]
rs12997568	0.81[AMR][1000 genomes]
rs13000788	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13003035	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13005729	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006448	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13013228	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13014700	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13015885	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13020517	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13022837	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13026192	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13031853	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13031866	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13033744	0.82[AMR][1000 genomes]
rs13383097	0.81[AMR][1000 genomes]
rs17350056	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17350125	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17350188	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17434634	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17434655	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1806683	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1815028	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2001436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006997	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2012574	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116367	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs2272051	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs2272178	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2280507	0.82[CHB][hapmap]
rs2421557	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421558	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2421559	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs2421574	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2421575	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421672	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421674	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421675	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421676	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2421677	0.82[EUR][1000 genomes]
rs35421685	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35498419	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35767294	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35791379	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3813228	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs3980695	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4241257	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4358149	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4513320	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4530394	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852311	0.82[CHB][hapmap]
rs4852316	0.90[EUR][1000 genomes]
rs4852966	0.90[EUR][1000 genomes]
rs4852967	0.87[EUR][1000 genomes]
rs4852972	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4852975	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4852976	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4852977	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4852978	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6732812	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6748233	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6749841	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750494	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6750515	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6750877	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6755500	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7210	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7368570	0.80[AMR][1000 genomes]
rs7370393	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7558546	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7591112	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7599453	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606947	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7608328	0.85[EUR][1000 genomes]
rs891695	0.84[AMR][1000 genomes]
rs9309475	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9309476	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12998980	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs12998980	TPRKB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr2:73902200-73931400	Weak transcription	Brain Anterior Caudate	brain
3	chr2:73926000-73931000	Enhancers	Fetal Intestine Small	intestine
4	chr2:73927000-73931400	Enhancers	Placenta	Placenta
5	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:73927200-73932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:73927800-73954800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:73928400-73936200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:73929200-73930800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:73929200-73936400	Enhancers	Fetal Intestine Large	intestine
12	chr2:73929400-73931000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:73929600-73930800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:73929800-73930800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:73929800-73930800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:73929800-73930800	Weak transcription	Spleen	Spleen
17	chr2:73929800-73931200	Enhancers	Liver	Liver
18	chr2:73929800-73931800	Weak transcription	K562	blood
19	chr2:73929800-73934200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:73929800-73934400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:73929800-73934600	Weak transcription	Colonic Mucosa	Colon
22	chr2:73930000-73930800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:73930200-73930800	Weak transcription	Fetal Heart	heart
24	chr2:73930400-73931200	Enhancers	Lung	lung
25	chr2:73930400-73932200	Enhancers	Ovary	ovary
26	chr2:73930600-73930800	Enhancers	Right Atrium	heart
27	chr2:73930600-73931000	Enhancers	Gastric	stomach
28	chr2:73930600-73931200	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:73930600-73932800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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