Variant report

Variant	rs6546835
Chromosome Location	chr2:73664715-73664716
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	chr2:73663877..73666460-chr2:73672462..73674821,2	MCF-7	breast:
2	chr2:73664466..73667206-chr2:73668584..73670663,2	K562	blood:

Extended variants
information (count: 167 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10169213	0.84[EUR][1000 genomes]
rs10169714	0.84[EUR][1000 genomes]
rs10170786	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173534	0.82[EUR][1000 genomes]
rs10178678	0.87[EUR][1000 genomes]
rs10179134	0.90[EUR][1000 genomes]
rs10181563	0.80[EUR][1000 genomes]
rs10183818	0.91[EUR][1000 genomes]
rs10184268	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185080	0.84[EUR][1000 genomes]
rs10186501	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.91[EUR][1000 genomes]
rs10187416	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10193972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195357	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195358	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197409	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197755	0.84[EUR][1000 genomes]
rs10198549	0.94[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs10199224	0.89[EUR][1000 genomes]
rs10207220	0.84[EUR][1000 genomes]
rs10207264	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469966	0.80[EUR][1000 genomes]
rs10496191	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496192	0.88[CEU][hapmap]
rs10496193	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052162	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126404	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114380	0.84[EUR][1000 genomes]
rs11674602	0.91[EUR][1000 genomes]
rs11676385	0.92[EUR][1000 genomes]
rs11679809	0.88[EUR][1000 genomes]
rs11686019	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689588	0.86[EUR][1000 genomes]
rs11693586	0.91[EUR][1000 genomes]
rs11693588	0.91[EUR][1000 genomes]
rs11884776	0.94[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs11899740	0.90[EUR][1000 genomes]
rs11899902	0.91[EUR][1000 genomes]
rs11901272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383871	0.90[EUR][1000 genomes]
rs13384952	0.91[EUR][1000 genomes]
rs13385564	0.89[EUR][1000 genomes]
rs13391258	1.00[ASN][1000 genomes]
rs13391552	0.82[EUR][1000 genomes]
rs13392691	0.90[EUR][1000 genomes]
rs13392872	0.90[EUR][1000 genomes]
rs13398956	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13400985	0.91[EUR][1000 genomes]
rs13409668	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13411311	0.91[EUR][1000 genomes]
rs13421462	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13427832	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428235	0.91[EUR][1000 genomes]
rs13431267	0.82[EUR][1000 genomes]
rs13432605	0.82[EUR][1000 genomes]
rs1403284	0.92[EUR][1000 genomes]
rs1403412	0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1534471	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009149	0.84[EUR][1000 genomes]
rs17009159	0.84[EUR][1000 genomes]
rs1881244	0.82[AFR][1000 genomes]
rs1881245	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918863	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017116	0.80[YRI][hapmap]
rs2056486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421550	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421552	0.89[EUR][1000 genomes]
rs2421555	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28879089	0.82[EUR][1000 genomes]
rs2901438	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738848	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813227	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4500972	0.87[ASN][1000 genomes]
rs56014217	0.91[EUR][1000 genomes]
rs56145559	0.86[EUR][1000 genomes]
rs56154726	0.91[EUR][1000 genomes]
rs56672945	0.91[EUR][1000 genomes]
rs58603761	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844734	0.91[EUR][1000 genomes]
rs62151646	0.93[EUR][1000 genomes]
rs62151652	0.93[EUR][1000 genomes]
rs6546827	0.88[CEU][hapmap];0.90[YRI][hapmap]
rs6546836	0.88[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546837	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546839	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546845	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546847	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546856	1.00[ASN][1000 genomes]
rs6546857	0.89[CEU][hapmap]
rs6546858	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546859	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6705977	1.00[ASN][1000 genomes]
rs6706409	0.85[MKK][hapmap];0.90[YRI][hapmap]
rs6707722	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708766	0.91[EUR][1000 genomes]
rs6710438	0.81[EUR][1000 genomes]
rs6711001	1.00[ASN][1000 genomes]
rs6711033	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6718843	1.00[ASN][1000 genomes]
rs6719753	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724782	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726694	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735946	0.84[EUR][1000 genomes]
rs6736866	0.95[EUR][1000 genomes]
rs6740223	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740766	0.84[EUR][1000 genomes]
rs6741067	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6745368	0.82[EUR][1000 genomes]
rs6745480	0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753344	0.95[EUR][1000 genomes]
rs6755217	0.92[EUR][1000 genomes]
rs6755241	0.92[EUR][1000 genomes]
rs6756885	0.94[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6756987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73947808	0.91[EUR][1000 genomes]
rs7424690	0.83[EUR][1000 genomes]
rs7558944	0.82[EUR][1000 genomes]
rs7564890	0.93[EUR][1000 genomes]
rs7566364	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566385	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567585	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.91[EUR][1000 genomes]
rs7576245	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580825	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs7582606	0.82[EUR][1000 genomes]
rs7583255	0.84[EUR][1000 genomes]
rs7584575	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585004	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585124	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586463	0.84[EUR][1000 genomes]
rs7588169	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7598396	0.95[EUR][1000 genomes]
rs7598419	0.84[EUR][1000 genomes]
rs7598946	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602980	0.91[EUR][1000 genomes]
rs7603647	0.82[EUR][1000 genomes]
rs7604682	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607892	0.82[EUR][1000 genomes]
rs9309473	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs9653557	0.84[EUR][1000 genomes]
rs9749859	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9750915	0.82[EUR][1000 genomes]
rs9753079	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807961	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6546835	ALMS1P	cis	cerebellum	SCAN
rs6546835	ALMS1	cis	cerebellum	SCAN
rs6546835	ALMS1P	cis	parietal	SCAN
rs6546835	ALMS1P	cis	Artery Tibial	GTEx
rs6546835	ALMS1	cis	normal skin	skin_eQTL
rs6546835	ALMS1	cis	parietal	SCAN
rs6546835	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546835	ALMS1P	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73637800-73676200	Weak transcription	Fetal Brain Male	brain
2	chr2:73639200-73675400	Weak transcription	HMEC	breast
3	chr2:73642200-73666000	Weak transcription	NHLF	lung
4	chr2:73645400-73675200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:73645600-73675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:73645600-73676600	Weak transcription	NH-A	brain
7	chr2:73645600-73685600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:73646400-73675200	Weak transcription	Osteobl	bone
9	chr2:73647000-73684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:73649600-73668000	Weak transcription	Gastric	stomach
11	chr2:73652000-73678400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:73652200-73688400	Weak transcription	Colonic Mucosa	Colon
13	chr2:73657200-73675400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:73658400-73676600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:73658800-73666200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:73659400-73675400	Weak transcription	Spleen	Spleen
17	chr2:73660200-73684400	Weak transcription	HUVEC	blood vessel
18	chr2:73661600-73665400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:73661800-73665000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr2:73661800-73665200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:73662200-73665200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:73662200-73665200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:73662200-73665800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:73662600-73664800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:73662600-73665000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:73662600-73665000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
27	chr2:73662600-73665200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:73662600-73665200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:73662600-73665200	Strong transcription	Rectal Smooth Muscle	rectum
30	chr2:73662800-73665200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:73662800-73665200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:73662800-73665200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:73662800-73665400	Strong transcription	Fetal Thymus	thymus
34	chr2:73662800-73665400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:73662800-73665400	Strong transcription	HSMM	muscle
36	chr2:73663000-73665000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:73663000-73665000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr2:73663000-73665400	Strong transcription	Placenta	Placenta
39	chr2:73663000-73668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:73663000-73674600	Weak transcription	Aorta	Aorta
41	chr2:73663000-73675200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:73663200-73665600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:73663200-73675200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:73663200-73675200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:73663400-73665200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:73663400-73675400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:73663400-73675400	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:73663600-73665400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:73663600-73665400	Strong transcription	Brain Anterior Caudate	brain
50	chr2:73663600-73665800	Strong transcription	Fetal Kidney	kidney

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