Variant report

Variant	rs11901272
Chromosome Location	chr2:73720444-73720445
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	chr2:73612074..73614842-chr2:73720180..73723169,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs10165862	1.00[YRI][hapmap]
rs10169213	0.81[EUR][1000 genomes]
rs10169714	0.81[EUR][1000 genomes]
rs10170786	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178678	0.83[EUR][1000 genomes]
rs10179134	0.82[EUR][1000 genomes]
rs10183818	0.87[EUR][1000 genomes]
rs10184268	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186501	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.87[EUR][1000 genomes]
rs10187416	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10193972	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10199224	0.85[EUR][1000 genomes]
rs10206899	0.94[CEU][hapmap]
rs10207220	0.81[EUR][1000 genomes]
rs10207264	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496191	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.81[EUR][1000 genomes]
rs11674602	0.88[EUR][1000 genomes]
rs11676385	0.88[EUR][1000 genomes]
rs11686019	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689588	0.83[EUR][1000 genomes]
rs11693586	0.88[EUR][1000 genomes]
rs11693588	0.88[EUR][1000 genomes]
rs11884776	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs11899740	0.82[EUR][1000 genomes]
rs11899902	0.83[EUR][1000 genomes]
rs11903916	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383871	0.82[EUR][1000 genomes]
rs13384952	0.89[EUR][1000 genomes]
rs13385564	0.86[EUR][1000 genomes]
rs13391258	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	0.86[EUR][1000 genomes]
rs13392872	0.86[EUR][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13400985	0.87[EUR][1000 genomes]
rs13409668	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	0.94[CEU][hapmap]
rs13411311	0.88[EUR][1000 genomes]
rs13421462	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13427832	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428235	0.83[EUR][1000 genomes]
rs13538	0.94[CEU][hapmap]
rs1403284	0.88[EUR][1000 genomes]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.81[EUR][1000 genomes]
rs17009159	0.81[EUR][1000 genomes]
rs1881245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.85[EUR][1000 genomes]
rs2421555	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901438	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs56014217	0.83[EUR][1000 genomes]
rs56154726	0.89[EUR][1000 genomes]
rs56672945	0.83[EUR][1000 genomes]
rs58603761	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844734	0.83[EUR][1000 genomes]
rs62151646	0.87[EUR][1000 genomes]
rs62151652	0.87[EUR][1000 genomes]
rs6546827	0.88[CEU][hapmap];0.80[YRI][hapmap]
rs6546835	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546856	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.89[CEU][hapmap]
rs6546858	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6704782	0.82[EUR][1000 genomes]
rs6705489	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6705977	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6707722	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.88[EUR][1000 genomes]
rs6711001	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6711033	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6718843	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6719753	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.81[EUR][1000 genomes]
rs6736866	0.85[EUR][1000 genomes]
rs6740223	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.81[EUR][1000 genomes]
rs6741067	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6745480	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753344	0.85[EUR][1000 genomes]
rs6755217	0.83[EUR][1000 genomes]
rs6755241	0.83[EUR][1000 genomes]
rs6756885	0.94[CEU][hapmap]
rs6756987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759452	0.82[CEU][hapmap]
rs73947808	0.89[EUR][1000 genomes]
rs7424690	0.81[EUR][1000 genomes]
rs7564890	0.84[EUR][1000 genomes]
rs7566364	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.89[EUR][1000 genomes]
rs7576245	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7583255	0.81[EUR][1000 genomes]
rs7584575	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.81[EUR][1000 genomes]
rs7588169	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7598396	0.85[EUR][1000 genomes]
rs7598419	0.81[EUR][1000 genomes]
rs7598946	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.87[EUR][1000 genomes]
rs7604682	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs9653557	0.81[EUR][1000 genomes]
rs9749859	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9753079	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11901272	ALMS1P	cis	Whole Blood	GTEx
rs11901272	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11901272	ALMS1	cis	normal skin	skin_eQTL
rs11901272	ALMS1P	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73704600-73721000	Weak transcription	HMEC	breast
2	chr2:73705800-73722600	Weak transcription	Brain Substantia Nigra	brain
3	chr2:73706600-73721000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:73707000-73733400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:73709200-73725400	Weak transcription	Fetal Brain Male	brain
6	chr2:73711800-73740400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:73713000-73721000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:73713000-73721000	Weak transcription	Small Intestine	intestine
9	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:73713400-73721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:73714600-73721200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:73714600-73725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:73714800-73721200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:73714800-73722200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:73715000-73721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:73715000-73724600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:73715200-73722600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:73715600-73720800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:73715600-73740200	Weak transcription	Esophagus	oesophagus
20	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:73715800-73720600	Weak transcription	GM12878-XiMat	blood
22	chr2:73715800-73721000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:73715800-73740200	Weak transcription	Gastric	stomach
24	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:73717800-73720600	Weak transcription	Fetal Stomach	stomach
26	chr2:73717800-73721000	Weak transcription	Psoas Muscle	Psoas
27	chr2:73718000-73721000	Weak transcription	NH-A	brain
28	chr2:73718000-73723400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:73718000-73727400	Weak transcription	Pancreas	Pancrea
30	chr2:73718000-73740800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:73718000-73746800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:73718200-73721000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:73718200-73721200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:73718200-73724200	Weak transcription	Brain Angular Gyrus	brain
35	chr2:73718200-73731800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:73718200-73740400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:73718400-73721000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:73718400-73721200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:73718400-73726800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:73718400-73738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:73718400-73740200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:73718600-73721200	Weak transcription	Lung	lung
43	chr2:73718600-73721800	Weak transcription	HepG2	liver
44	chr2:73718600-73732400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:73718600-73740200	Weak transcription	Fetal Kidney	kidney
46	chr2:73718600-73740400	Weak transcription	Thymus	Thymus
47	chr2:73718800-73720600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:73718800-73720600	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:73718800-73721200	Weak transcription	A549	lung
50	chr2:73718800-73722800	Weak transcription	Fetal Muscle Trunk	muscle

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