Variant report

Variant	rs6546857
Chromosome Location	chr2:73837955-73837956
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	chr2:73837883..73840443-chr2:74211046..74212867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10168931	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10169213	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169714	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170786	0.88[EUR][1000 genomes]
rs10173534	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178409	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10178678	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179134	1.00[ASN][1000 genomes]
rs10181563	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183818	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185080	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10193972	0.89[CEU][hapmap]
rs10197409	0.86[EUR][1000 genomes]
rs10197755	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198549	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199224	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206899	0.94[CEU][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs10207220	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.92[EUR][1000 genomes]
rs10469966	1.00[ASN][1000 genomes]
rs10496192	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10496193	0.84[EUR][1000 genomes]
rs1052162	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11126404	0.80[EUR][1000 genomes]
rs1114380	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674602	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675958	1.00[ASN][1000 genomes]
rs11676385	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679594	1.00[ASN][1000 genomes]
rs11679809	1.00[ASN][1000 genomes]
rs11680965	1.00[ASN][1000 genomes]
rs11686019	0.81[EUR][1000 genomes]
rs11686541	1.00[ASN][1000 genomes]
rs11689164	1.00[ASN][1000 genomes]
rs11689588	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693586	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693588	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884776	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893881	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899740	1.00[ASN][1000 genomes]
rs11899902	1.00[ASN][1000 genomes]
rs11901272	0.89[CEU][hapmap]
rs11903916	0.88[EUR][1000 genomes]
rs13383871	1.00[ASN][1000 genomes]
rs13384756	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13384952	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385564	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391258	0.83[EUR][1000 genomes]
rs13391552	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392691	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392872	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398956	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400985	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409366	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13410232	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13411311	0.83[EUR][1000 genomes]
rs13421462	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427832	0.92[EUR][1000 genomes]
rs13428235	1.00[ASN][1000 genomes]
rs13431267	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431529	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13432605	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13538	0.94[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1403284	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534471	0.89[CEU][hapmap]
rs1589576	1.00[ASN][1000 genomes]
rs17009149	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009159	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349321	1.00[ASN][1000 genomes]
rs1881245	0.89[CEU][hapmap]
rs2056486	0.89[CEU][hapmap]
rs2421550	0.89[CEU][hapmap]
rs2421552	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421555	0.88[EUR][1000 genomes]
rs2421577	0.92[EUR][1000 genomes]
rs2567598	1.00[ASN][1000 genomes]
rs2567601	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2567602	1.00[ASN][1000 genomes]
rs2567603	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28879089	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547554	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56014217	1.00[ASN][1000 genomes]
rs56154726	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56672945	1.00[ASN][1000 genomes]
rs60844734	1.00[ASN][1000 genomes]
rs62149774	1.00[ASN][1000 genomes]
rs62149777	1.00[ASN][1000 genomes]
rs62149781	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149782	1.00[ASN][1000 genomes]
rs62149804	1.00[ASN][1000 genomes]
rs62151646	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62151652	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153182	1.00[ASN][1000 genomes]
rs62153183	1.00[ASN][1000 genomes]
rs6546837	0.89[CEU][hapmap]
rs6546838	0.89[CEU][hapmap]
rs6546839	0.89[CEU][hapmap]
rs6546845	0.84[EUR][1000 genomes]
rs6546847	0.86[EUR][1000 genomes]
rs6546849	0.91[EUR][1000 genomes]
rs6546850	0.91[EUR][1000 genomes]
rs6546851	0.91[EUR][1000 genomes]
rs6546852	0.91[EUR][1000 genomes]
rs6546853	0.91[EUR][1000 genomes]
rs6546854	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546856	0.94[EUR][1000 genomes]
rs6546858	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs6546859	0.92[EUR][1000 genomes]
rs6546860	0.92[EUR][1000 genomes]
rs6546861	0.83[EUR][1000 genomes]
rs6704782	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705489	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705977	0.83[EUR][1000 genomes]
rs6708766	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710438	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711001	0.83[EUR][1000 genomes]
rs6711033	0.94[CEU][hapmap]
rs6718843	0.82[EUR][1000 genomes]
rs6723247	0.92[EUR][1000 genomes]
rs6724782	0.89[CEU][hapmap]
rs6726694	0.92[EUR][1000 genomes]
rs6735946	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736866	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744398	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6745368	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745480	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs6753344	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755217	1.00[ASN][1000 genomes]
rs6755241	1.00[ASN][1000 genomes]
rs6756885	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756987	0.89[CEU][hapmap]
rs6759452	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73947808	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424690	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558944	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564890	1.00[ASN][1000 genomes]
rs7566364	0.92[EUR][1000 genomes]
rs7572722	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576245	0.91[EUR][1000 genomes]
rs7580750	0.86[EUR][1000 genomes]
rs7580825	1.00[ASN][1000 genomes]
rs7582051	1.00[ASN][1000 genomes]
rs7582606	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583255	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587577	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.89[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596773	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598396	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598419	0.91[EUR][1000 genomes]
rs7602980	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603647	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604682	0.86[EUR][1000 genomes]
rs7607892	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309473	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs9653557	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749859	0.88[EUR][1000 genomes]
rs9750915	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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	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	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Metabolite levels (X-11787)	23934736	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6546857	ALMS1P	cis	Esophagus Muscularis	GTEx
rs6546857	ALMS1P	cis	Nerve Tibial	GTEx
rs6546857	ALMS1	cis	normal skin	skin_eQTL
rs6546857	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546857	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6546857	ALMS1P	cis	Thyroid	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
2	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
3	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
4	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
6	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:73827000-73840600	Weak transcription	NHLF	lung
11	chr2:73827600-73838200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:73829000-73839000	Weak transcription	NHDF-Ad	bronchial
15	chr2:73829000-73839400	Weak transcription	Placenta	Placenta
16	chr2:73829200-73838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:73829200-73840000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:73829600-73840200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:73829800-73838000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:73829800-73839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:73829800-73840000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:73829800-73840000	Weak transcription	Gastric	stomach
24	chr2:73829800-73840400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:73830000-73840800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:73830200-73838000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr2:73830400-73839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:73830400-73843600	Weak transcription	Aorta	Aorta
29	chr2:73830600-73838000	Weak transcription	GM12878-XiMat	blood
30	chr2:73830600-73838000	Weak transcription	HSMMtube	muscle
31	chr2:73830600-73838800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:73830600-73839000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:73830600-73839000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:73830600-73839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:73830600-73840000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:73830600-73841200	Weak transcription	Liver	Liver
37	chr2:73830600-73843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:73830600-73847600	Weak transcription	Spleen	Spleen
39	chr2:73830600-73854800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:73830800-73839200	Weak transcription	Osteobl	bone
41	chr2:73830800-73840800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:73831000-73838000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:73831000-73842200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:73831200-73839600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:73831200-73841200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:73832600-73838000	Weak transcription	Brain Angular Gyrus	brain
47	chr2:73833800-73839200	Strong transcription	Fetal Brain Female	brain
48	chr2:73835200-73838600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:73835400-73838400	Strong transcription	Left Ventricle	heart
50	chr2:73835400-73838400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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