Variant report

Variant	rs6546849
Chromosome Location	chr2:73831037-73831038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 165 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10169213	0.89[EUR][1000 genomes]
rs10169714	0.89[EUR][1000 genomes]
rs10170786	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.91[EUR][1000 genomes]
rs10178409	0.86[EUR][1000 genomes]
rs10178678	0.83[EUR][1000 genomes]
rs10181563	0.84[EUR][1000 genomes]
rs10183818	0.80[EUR][1000 genomes]
rs10184268	1.00[ASN][1000 genomes]
rs10185080	0.88[EUR][1000 genomes]
rs10186501	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.80[EUR][1000 genomes]
rs10187416	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	0.94[CEU][hapmap]
rs10193972	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	1.00[ASN][1000 genomes]
rs10195358	1.00[ASN][1000 genomes]
rs10197409	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.88[EUR][1000 genomes]
rs10198549	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10199224	0.82[EUR][1000 genomes]
rs10206899	1.00[CEU][hapmap]
rs10207220	0.89[EUR][1000 genomes]
rs10207264	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496191	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.83[CEU][hapmap]
rs10496193	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.89[EUR][1000 genomes]
rs11674602	0.81[EUR][1000 genomes]
rs11676385	0.81[EUR][1000 genomes]
rs11686019	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	1.00[ASN][1000 genomes]
rs11689588	0.87[EUR][1000 genomes]
rs11693586	0.81[EUR][1000 genomes]
rs11693588	0.81[EUR][1000 genomes]
rs11884776	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11893881	0.94[EUR][1000 genomes]
rs11901272	0.94[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.82[EUR][1000 genomes]
rs13385564	0.80[EUR][1000 genomes]
rs13391258	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391552	0.90[EUR][1000 genomes]
rs13392691	0.82[EUR][1000 genomes]
rs13398956	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13400985	0.80[EUR][1000 genomes]
rs13409366	0.94[EUR][1000 genomes]
rs13409668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	1.00[CEU][hapmap]
rs13411311	0.81[EUR][1000 genomes]
rs13421462	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13427832	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431267	0.86[EUR][1000 genomes]
rs13432605	0.91[EUR][1000 genomes]
rs13538	1.00[CEU][hapmap]
rs1403284	0.81[EUR][1000 genomes]
rs1534471	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.89[EUR][1000 genomes]
rs17009159	0.89[EUR][1000 genomes]
rs1881245	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	1.00[ASN][1000 genomes]
rs2056486	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280506	0.83[YRI][hapmap]
rs2421550	0.94[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.82[EUR][1000 genomes]
rs2421555	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.90[EUR][1000 genomes]
rs2901438	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2947845	0.84[YRI][hapmap]
rs2948441	0.84[YRI][hapmap]
rs3738848	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs4627598	0.84[YRI][hapmap]
rs4852311	0.82[YRI][hapmap]
rs56154726	0.82[EUR][1000 genomes]
rs58603761	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149781	0.87[EUR][1000 genomes]
rs6546835	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546836	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546854	0.94[EUR][1000 genomes]
rs6546856	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs6546858	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	0.94[CEU][hapmap]
rs6705977	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707722	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.81[EUR][1000 genomes]
rs6710438	0.91[EUR][1000 genomes]
rs6711001	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6718843	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719753	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.89[EUR][1000 genomes]
rs6740223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.89[EUR][1000 genomes]
rs6744273	0.84[YRI][hapmap]
rs6745368	0.91[EUR][1000 genomes]
rs6745480	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756885	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6756987	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759452	0.89[CEU][hapmap]
rs73947808	0.82[EUR][1000 genomes]
rs7424690	0.87[EUR][1000 genomes]
rs7558944	0.91[EUR][1000 genomes]
rs7566364	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.82[EUR][1000 genomes]
rs7576245	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	0.94[CEU][hapmap]
rs7582606	0.91[EUR][1000 genomes]
rs7583255	0.89[EUR][1000 genomes]
rs7584575	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.89[EUR][1000 genomes]
rs7587577	0.94[EUR][1000 genomes]
rs7588169	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.94[CEU][hapmap]
rs7596773	0.94[EUR][1000 genomes]
rs7598419	0.89[EUR][1000 genomes]
rs7598946	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.80[EUR][1000 genomes]
rs7603647	0.90[EUR][1000 genomes]
rs7604682	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.90[EUR][1000 genomes]
rs7607989	0.83[YRI][hapmap]
rs9309473	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9653557	0.89[EUR][1000 genomes]
rs9749859	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.91[EUR][1000 genomes]
rs9753079	1.00[ASN][1000 genomes]
rs9807961	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	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
6	nsv961795	chr2:73830604-73834098	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6546849	ALMS1P	cis	Thyroid	GTEx
rs6546849	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546849	ALMS1	cis	normal skin	skin_eQTL
rs6546849	ALMS1P	cis	Artery Tibial	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
2	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
3	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
4	chr2:73815600-73836000	Weak transcription	A549	lung
5	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
6	chr2:73822600-73833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:73825400-73833600	Weak transcription	Esophagus	oesophagus
10	chr2:73826000-73832200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:73826200-73833200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:73826800-73832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:73827000-73840600	Weak transcription	NHLF	lung
18	chr2:73827200-73831200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:73827200-73831600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:73827200-73837200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:73827400-73836400	Strong transcription	Primary T cells from cord blood	blood
22	chr2:73827600-73831800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:73827600-73832400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:73827600-73837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:73827600-73838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:73827800-73832200	Strong transcription	Fetal Intestine Large	intestine
28	chr2:73827800-73832200	Strong transcription	Left Ventricle	heart
29	chr2:73827800-73832200	Strong transcription	Dnd41	blood
30	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:73828000-73832400	Strong transcription	Adipose Nuclei	Adipose
32	chr2:73828200-73831200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:73828400-73831200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:73828400-73832200	Strong transcription	Fetal Lung	lung
35	chr2:73828400-73832400	Weak transcription	Small Intestine	intestine
36	chr2:73828800-73837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:73829000-73831200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:73829000-73837600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:73829000-73839000	Weak transcription	NHDF-Ad	bronchial
40	chr2:73829000-73839400	Weak transcription	Placenta	Placenta
41	chr2:73829200-73838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:73829200-73840000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:73829600-73833600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:73829600-73835600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:73829600-73837200	Weak transcription	Lung	lung
47	chr2:73829600-73837600	Weak transcription	Pancreas	Pancrea
48	chr2:73829600-73840200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:73829800-73832200	Weak transcription	Colonic Mucosa	Colon
50	chr2:73829800-73835400	Weak transcription	Right Ventricle	heart

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