Variant report

Variant	rs6711033
Chromosome Location	chr2:73746643-73746644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs10169213	0.86[EUR][1000 genomes]
rs10169714	0.87[EUR][1000 genomes]
rs10170786	0.89[EUR][1000 genomes]
rs10170849	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10173534	0.86[EUR][1000 genomes]
rs10178678	0.89[EUR][1000 genomes]
rs10179134	0.84[EUR][1000 genomes]
rs10181563	0.82[EUR][1000 genomes]
rs10183818	0.91[EUR][1000 genomes]
rs10184268	0.86[EUR][1000 genomes]
rs10185080	0.86[EUR][1000 genomes]
rs10186501	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10187192	0.91[EUR][1000 genomes]
rs10187416	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10189574	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10190219	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs10193972	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10195357	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10195358	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10197409	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10197755	0.86[EUR][1000 genomes]
rs10198549	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10199224	0.91[EUR][1000 genomes]
rs10206899	1.00[CEU][hapmap]
rs10207220	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10207264	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10209517	0.85[EUR][1000 genomes]
rs10469966	0.82[EUR][1000 genomes]
rs10496191	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10496192	0.83[CEU][hapmap]
rs10496193	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1052162	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11126404	0.84[EUR][1000 genomes]
rs1114380	0.86[EUR][1000 genomes]
rs11674602	0.91[EUR][1000 genomes]
rs11676385	0.91[EUR][1000 genomes]
rs11679809	0.82[EUR][1000 genomes]
rs11686019	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11689392	0.87[EUR][1000 genomes]
rs11689588	0.89[EUR][1000 genomes]
rs11693586	0.91[EUR][1000 genomes]
rs11693588	0.91[EUR][1000 genomes]
rs11884776	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs11893881	0.82[EUR][1000 genomes]
rs11899740	0.84[EUR][1000 genomes]
rs11899902	0.83[EUR][1000 genomes]
rs11901272	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11903916	0.89[EUR][1000 genomes]
rs13383871	0.84[EUR][1000 genomes]
rs13384952	0.92[EUR][1000 genomes]
rs13385564	0.89[EUR][1000 genomes]
rs13391552	0.85[EUR][1000 genomes]
rs13392691	0.92[EUR][1000 genomes]
rs13392872	0.89[EUR][1000 genomes]
rs13398956	0.94[CEU][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes]
rs13400985	0.91[EUR][1000 genomes]
rs13409366	0.82[EUR][1000 genomes]
rs13409668	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13410232	1.00[CEU][hapmap]
rs13411311	0.91[EUR][1000 genomes]
rs13421462	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs13427832	0.85[EUR][1000 genomes]
rs13428235	0.83[EUR][1000 genomes]
rs13431267	0.88[EUR][1000 genomes]
rs13432605	0.86[EUR][1000 genomes]
rs13538	1.00[CEU][hapmap]
rs1403284	0.91[EUR][1000 genomes]
rs1534471	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17009149	0.86[EUR][1000 genomes]
rs17009159	0.86[EUR][1000 genomes]
rs1881245	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1918863	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2056486	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2140195	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2421550	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2421552	0.91[EUR][1000 genomes]
rs2421555	0.89[EUR][1000 genomes]
rs2421577	0.85[EUR][1000 genomes]
rs28879089	0.85[EUR][1000 genomes]
rs2901438	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738848	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3813227	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56014217	0.84[EUR][1000 genomes]
rs56154726	0.92[EUR][1000 genomes]
rs56672945	0.84[EUR][1000 genomes]
rs58603761	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60844734	0.84[EUR][1000 genomes]
rs62149781	0.82[EUR][1000 genomes]
rs62151646	0.90[EUR][1000 genomes]
rs62151652	0.90[EUR][1000 genomes]
rs6546827	0.83[CEU][hapmap]
rs6546835	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546836	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546837	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546838	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546839	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6546845	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6546847	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6546849	0.85[EUR][1000 genomes]
rs6546850	0.86[EUR][1000 genomes]
rs6546851	0.86[EUR][1000 genomes]
rs6546852	0.86[EUR][1000 genomes]
rs6546853	0.86[EUR][1000 genomes]
rs6546854	0.82[EUR][1000 genomes]
rs6546856	0.82[EUR][1000 genomes]
rs6546857	0.94[CEU][hapmap]
rs6546858	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6546859	0.85[EUR][1000 genomes]
rs6546860	0.85[EUR][1000 genomes]
rs6704782	0.88[EUR][1000 genomes]
rs6705489	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6707722	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6708766	0.91[EUR][1000 genomes]
rs6710438	0.84[EUR][1000 genomes]
rs6719753	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6723247	0.85[EUR][1000 genomes]
rs6724782	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6726694	0.85[EUR][1000 genomes]
rs6735946	0.86[EUR][1000 genomes]
rs6736866	0.89[EUR][1000 genomes]
rs6740223	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6740766	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6741067	0.82[EUR][1000 genomes]
rs6745368	0.86[EUR][1000 genomes]
rs6745480	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6753344	0.89[EUR][1000 genomes]
rs6755217	0.86[EUR][1000 genomes]
rs6755241	0.86[EUR][1000 genomes]
rs6756885	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6756987	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6759452	0.89[CEU][hapmap]
rs73947808	0.92[EUR][1000 genomes]
rs7424690	0.86[EUR][1000 genomes]
rs7558944	0.86[EUR][1000 genomes]
rs7564890	0.87[EUR][1000 genomes]
rs7566364	0.85[EUR][1000 genomes]
rs7566385	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7567585	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7572722	0.92[EUR][1000 genomes]
rs7576245	0.86[EUR][1000 genomes]
rs7580750	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7580825	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7582606	0.86[EUR][1000 genomes]
rs7583255	0.86[EUR][1000 genomes]
rs7584575	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7585004	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7585124	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7586463	0.86[EUR][1000 genomes]
rs7587577	0.82[EUR][1000 genomes]
rs7588169	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7594511	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7596773	0.82[EUR][1000 genomes]
rs7598396	0.89[EUR][1000 genomes]
rs7598419	0.86[EUR][1000 genomes]
rs7598946	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7602980	0.91[EUR][1000 genomes]
rs7603647	0.85[EUR][1000 genomes]
rs7604682	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7607014	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7607892	0.85[EUR][1000 genomes]
rs9309473	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9653557	0.86[EUR][1000 genomes]
rs9749859	0.89[EUR][1000 genomes]
rs9750915	0.86[EUR][1000 genomes]
rs9753079	0.86[EUR][1000 genomes]
rs9807961	0.87[AMR][1000 genomes];0.92[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6711033	ALMS1P	cis	Whole Blood	GTEx
rs6711033	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6711033	ALMS1	cis	normal skin	skin_eQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:73718000-73746800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:73719400-73747000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:73728200-73747000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:73731600-73759000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:73731800-73746800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:73731800-73752000	Weak transcription	Fetal Heart	heart
10	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
11	chr2:73736400-73761600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:73736800-73747400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:73737600-73747400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:73737600-73750600	Weak transcription	Small Intestine	intestine
15	chr2:73738000-73746800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:73738600-73746800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:73738800-73750200	Weak transcription	Stomach Mucosa	stomach
18	chr2:73739400-73756400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:73740000-73747000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:73740600-73746800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:73740600-73747000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:73740600-73747000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:73740800-73747400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:73740800-73752600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:73740800-73752800	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:73740800-73753800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:73740800-73757600	Weak transcription	Ovary	ovary
28	chr2:73741000-73747000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:73741000-73747000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:73741000-73748400	Weak transcription	Fetal Lung	lung
31	chr2:73741000-73748800	Weak transcription	Esophagus	oesophagus
32	chr2:73741000-73749200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:73741000-73750200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:73741000-73751000	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:73741000-73751800	Weak transcription	Fetal Kidney	kidney
36	chr2:73741000-73752200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:73741000-73752200	Weak transcription	Brain Substantia Nigra	brain
38	chr2:73741000-73752200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:73741000-73752600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:73741000-73755000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:73741000-73755600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:73741000-73756200	Weak transcription	Fetal Intestine Small	intestine
43	chr2:73741000-73756400	Weak transcription	Thymus	Thymus
44	chr2:73741000-73757200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:73741000-73757400	Weak transcription	Aorta	Aorta
46	chr2:73741000-73757400	Weak transcription	Pancreas	Pancrea
47	chr2:73741000-73757600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:73741000-73757800	Weak transcription	Gastric	stomach
49	chr2:73741000-73758800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:73741000-73759400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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