Variant report

Variant	rs11126414
Chromosome Location	chr2:73932044-73932045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73868945..73872912-chr2:73927731..73932752,4	MCF-7	breast:
2	chr2:73931503..73934295-chr2:73936024..73937687,2	MCF-7	breast:
3	chr2:73927692..73931050-chr2:73931884..73934947,3	K562	blood:
4	chr2:73920861..73923082-chr2:73929614..73932212,2	K562	blood:

Variant related genes	Relation type
ENSG00000144035	Chromatin interaction
ENSG00000204872	Chromatin interaction
ENSG00000163016	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10172044	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10190002	0.81[TSI][hapmap]
rs10191988	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10200762	0.93[EUR][1000 genomes]
rs10208995	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1052161	0.81[TSI][hapmap]
rs10865398	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs11126415	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11126416	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11126417	0.87[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11689234	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs11891140	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11892172	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11894953	0.87[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12052539	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12053242	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12233112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478871	0.91[CHB][hapmap]
rs12611487	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12612423	0.86[AMR][1000 genomes]
rs12615807	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12618600	0.85[TSI][hapmap]
rs12619258	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12624267	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713788	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12713789	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713790	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713791	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713793	0.87[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713794	0.84[EUR][1000 genomes]
rs12713795	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713797	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12713798	0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12992607	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12997018	0.84[EUR][1000 genomes]
rs12997568	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12998980	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]
rs13000788	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13003035	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13005729	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006448	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13013228	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13014700	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13015885	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13017182	0.84[GIH][hapmap];0.88[TSI][hapmap]
rs13020517	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13022837	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13026192	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13031853	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13031866	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13033744	1.00[GIH][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs1320374	0.81[TSI][hapmap]
rs13383097	0.83[AMR][1000 genomes]
rs17350056	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17350125	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17350188	0.87[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17434634	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17434655	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1806683	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1815028	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006997	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2012574	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116367	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs2272051	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs2272178	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2280507	0.81[CHB][hapmap]
rs2421557	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421558	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421559	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs2421574	0.83[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2421575	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2421586	0.83[TSI][hapmap]
rs2421668	0.83[TSI][hapmap]
rs2421672	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421674	0.87[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421675	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421676	0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2421677	0.83[EUR][1000 genomes]
rs35421685	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35498419	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35767294	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35791379	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3813228	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs3980695	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4241257	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4358149	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4513320	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4530394	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852311	0.81[CHB][hapmap]
rs4852316	0.91[EUR][1000 genomes]
rs4852966	0.88[EUR][1000 genomes]
rs4852967	0.86[EUR][1000 genomes]
rs4852972	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4852975	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4852976	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4852977	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4852978	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732812	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745560	0.82[GIH][hapmap];0.86[TSI][hapmap]
rs6748233	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6749841	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6750494	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750515	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750877	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6755500	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7210	0.87[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7368570	0.82[AMR][1000 genomes]
rs7370393	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7558546	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7570683	0.83[TSI][hapmap]
rs7591112	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7597302	0.81[AMR][1000 genomes]
rs7599453	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7606947	0.83[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7608328	0.84[EUR][1000 genomes]
rs891695	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9309475	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9309476	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11126414	ALMS1P	cis	parietal	SCAN
rs11126414	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs11126414	DUSP11	cis	parietal	SCAN
rs11126414	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11126414	ALMS1	cis	parietal	SCAN
rs11126414	STAMBP	cis	parietal	SCAN
rs11126414	ALMS1	cis	cerebellum	SCAN
rs11126414	DUSP11	cis	cerebellum	SCAN
rs11126414	ALMS1P	cis	cerebellum	SCAN

Chromatin state (count:17 , 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	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells	blood
3	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:73927200-73932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:73927800-73954800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:73928400-73936200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:73929200-73936400	Enhancers	Fetal Intestine Large	intestine
8	chr2:73929800-73934200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:73929800-73934400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:73929800-73934600	Weak transcription	Colonic Mucosa	Colon
11	chr2:73930400-73932200	Enhancers	Ovary	ovary
12	chr2:73930600-73932800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr2:73931000-73933800	Weak transcription	Fetal Intestine Small	intestine
14	chr2:73931200-73932200	Weak transcription	Lung	lung
15	chr2:73931400-73932400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:73931800-73932200	Enhancers	Fetal Muscle Leg	muscle
17	chr2:73931800-73932200	Enhancers	K562	blood

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