Variant report

Variant	rs11126417
Chromosome Location	chr2:73974315-73974316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73962788..73968740-chr2:73972105..73977482,12	MCF-7	breast:
2	chr2:73963856..73966240-chr2:73974280..73976997,3	MCF-7	breast:
3	chr2:73970816..73973211-chr2:73974076..73976705,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144034	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10172044	0.98[EUR][1000 genomes]
rs10190002	0.84[GIH][hapmap];0.81[TSI][hapmap]
rs10191988	0.94[EUR][1000 genomes]
rs10193032	0.83[TSI][hapmap]
rs10203740	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10208995	0.99[EUR][1000 genomes]
rs1052161	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11126414	0.87[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11126415	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11126416	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes]
rs11891140	0.93[EUR][1000 genomes]
rs11892172	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs11894953	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12052539	0.89[EUR][1000 genomes]
rs12053242	0.89[EUR][1000 genomes]
rs12233112	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12233115	0.83[EUR][1000 genomes]
rs12611487	0.80[EUR][1000 genomes]
rs12612423	0.81[EUR][1000 genomes]
rs12615807	0.94[EUR][1000 genomes]
rs12618600	0.83[GIH][hapmap];0.83[TSI][hapmap]
rs12619258	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12624267	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12713788	0.83[EUR][1000 genomes]
rs12713789	0.93[EUR][1000 genomes]
rs12713790	0.93[EUR][1000 genomes]
rs12713791	0.93[EUR][1000 genomes]
rs12713793	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12713794	0.89[EUR][1000 genomes]
rs12713795	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12713797	0.96[EUR][1000 genomes]
rs12713798	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12992607	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12997568	0.86[EUR][1000 genomes]
rs12998980	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs13000788	0.81[EUR][1000 genomes]
rs13003035	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs13005729	0.83[EUR][1000 genomes]
rs13006448	0.83[EUR][1000 genomes]
rs13006598	0.93[EUR][1000 genomes]
rs13013228	0.83[EUR][1000 genomes]
rs13014700	0.82[EUR][1000 genomes]
rs13015885	0.82[EUR][1000 genomes]
rs13020517	0.88[EUR][1000 genomes]
rs13031853	0.83[EUR][1000 genomes]
rs13031866	0.83[EUR][1000 genomes]
rs13033744	0.91[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs1320374	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs13383097	0.92[EUR][1000 genomes]
rs17350056	0.83[EUR][1000 genomes]
rs17350125	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs17350188	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17434634	0.83[EUR][1000 genomes]
rs17434655	0.83[EUR][1000 genomes]
rs1806683	0.90[EUR][1000 genomes]
rs1815028	0.90[EUR][1000 genomes]
rs2001436	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2001490	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2006997	0.94[EUR][1000 genomes]
rs2012574	0.83[EUR][1000 genomes]
rs2116367	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs2272051	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2272178	0.99[EUR][1000 genomes]
rs2421557	0.90[EUR][1000 genomes]
rs2421558	0.89[EUR][1000 genomes]
rs2421559	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2421574	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs2421575	0.82[EUR][1000 genomes]
rs2421586	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2421668	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs2421672	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs2421674	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2421675	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2421676	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2421677	0.94[EUR][1000 genomes]
rs2462127	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs35498419	0.89[EUR][1000 genomes]
rs35767294	0.83[EUR][1000 genomes]
rs35791379	0.98[EUR][1000 genomes]
rs3813228	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs3980695	0.90[EUR][1000 genomes]
rs4241257	0.90[EUR][1000 genomes]
rs4358149	0.94[EUR][1000 genomes]
rs4513320	0.83[EUR][1000 genomes]
rs4530394	0.83[EUR][1000 genomes]
rs4852316	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4852972	0.81[EUR][1000 genomes]
rs4852975	0.87[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs4852976	0.91[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4852977	0.90[EUR][1000 genomes]
rs4852978	0.93[EUR][1000 genomes]
rs6732812	0.83[EUR][1000 genomes]
rs6748233	0.90[EUR][1000 genomes]
rs6749841	0.93[EUR][1000 genomes]
rs6750494	0.95[EUR][1000 genomes]
rs6750515	0.95[EUR][1000 genomes]
rs6750877	0.88[EUR][1000 genomes]
rs6755500	0.93[EUR][1000 genomes]
rs7210	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs732778	0.87[EUR][1000 genomes]
rs7370393	0.83[EUR][1000 genomes]
rs7558546	0.89[EUR][1000 genomes]
rs7570683	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs7591112	0.93[EUR][1000 genomes]
rs7597302	0.92[EUR][1000 genomes]
rs7599453	0.89[EUR][1000 genomes]
rs7606947	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs891695	0.95[EUR][1000 genomes]
rs891696	0.90[EUR][1000 genomes]
rs9309475	0.98[EUR][1000 genomes]
rs9309476	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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
rs11126417	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs11126417	ALMS1	cis	cerebellum	SCAN
rs11126417	ALMS1	cis	parietal	SCAN
rs11126417	DUSP11	cis	parietal	SCAN
rs11126417	ALMS1P	cis	Nerve Tibial	GTEx
rs11126417	ALMS1P	cis	parietal	SCAN
rs11126417	DUSP11	cis	cerebellum	SCAN
rs11126417	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11126417	CGI-121	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73964600-74005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:73965000-73978800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:73965000-73993000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:73965400-73982200	Weak transcription	Hela-S3	cervix
5	chr2:73965400-73985600	Weak transcription	Fetal Heart	heart
6	chr2:73965400-73986200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:73965400-73986600	Weak transcription	Psoas Muscle	Psoas
8	chr2:73966200-73992000	Weak transcription	Stomach Mucosa	stomach
9	chr2:73967600-73978800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:73969400-73977000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:73969400-73983400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:73969400-73987200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:73969600-73986000	Weak transcription	Right Ventricle	heart
14	chr2:73969800-73982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:73969800-73982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:73970400-73974400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:73970400-73981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:73971000-73975600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:73971000-73976200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:73971200-73974400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:73971200-73974400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:73971200-73974400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:73971200-73974400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:73971200-73974400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:73971200-73974400	Strong transcription	Liver	Liver
26	chr2:73971200-73974400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:73971200-73974400	Strong transcription	NH-A	brain
28	chr2:73971200-73974800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:73971200-73975600	Strong transcription	Primary T cells from cord blood	blood
30	chr2:73971400-73974400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:73971400-73974400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:73971400-73974400	Strong transcription	Adipose Nuclei	Adipose
33	chr2:73971400-73974400	Strong transcription	Placenta	Placenta
34	chr2:73971400-73974400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:73971400-73974600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:73971400-73975600	Strong transcription	HSMM	muscle
37	chr2:73971400-73975600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:73971400-74002200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:73971600-73987000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:73971800-73974400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr2:73972000-73978800	Weak transcription	Brain Anterior Caudate	brain
42	chr2:73972000-73992200	Weak transcription	Fetal Kidney	kidney
43	chr2:73973000-73974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:73973000-73974400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:73973000-73974400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:73973000-73974400	Strong transcription	Fetal Thymus	thymus
47	chr2:73973000-73975000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:73973000-73975800	Strong transcription	Fetal Stomach	stomach
49	chr2:73973200-73974400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:73973200-73974400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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