Variant report

Variant	rs6546858
Chromosome Location	chr2:73838613-73838614
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: 167 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs10169213	0.89[EUR][1000 genomes]
rs10169714	0.89[EUR][1000 genomes]
rs10170786	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170849	0.88[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	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187192	0.80[EUR][1000 genomes]
rs10187416	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189574	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190219	0.94[CEU][hapmap]
rs10193972	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];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	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209517	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[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	0.85[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];0.95[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	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689392	1.00[ASN][1000 genomes]
rs11689588	0.86[EUR][1000 genomes]
rs11693586	0.81[EUR][1000 genomes]
rs11693588	0.81[EUR][1000 genomes]
rs11884776	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11893881	0.93[EUR][1000 genomes]
rs11901272	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903916	0.88[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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[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	0.95[EUR][1000 genomes]
rs13409668	0.81[AMR][1000 genomes];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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140195	0.82[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	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421577	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	0.83[YRI][hapmap]
rs2948441	0.83[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	0.83[YRI][hapmap]
rs4852311	0.80[YRI][hapmap]
rs56154726	0.82[EUR][1000 genomes]
rs58603761	0.86[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	0.82[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	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546849	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546850	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546851	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546852	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546853	0.97[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	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546857	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs6546859	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546860	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546861	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704782	0.86[EUR][1000 genomes]
rs6705489	0.94[CEU][hapmap]
rs6705977	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[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	0.81[AFR][1000 genomes];0.95[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	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719753	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723247	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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	0.95[AMR][1000 genomes];1.00[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	0.83[YRI][hapmap]
rs6745368	0.91[EUR][1000 genomes]
rs6745480	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.88[CEU][hapmap]
rs73947808	0.82[EUR][1000 genomes]
rs7424690	0.87[EUR][1000 genomes]
rs7558944	0.91[EUR][1000 genomes]
rs7566364	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572722	0.82[EUR][1000 genomes]
rs7576245	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580750	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594511	0.94[CEU][hapmap]
rs7596773	0.95[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	0.85[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	0.82[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:9 , 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
9	nsv10013	chr2:73838181-73841175	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6546858	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546858	ALMS1P	cis	Artery Tibial	GTEx
rs6546858	ALMS1P	cis	Skin Sun Exposed Lower leg	GTEx
rs6546858	ALMS1	cis	normal skin	skin_eQTL
rs6546858	ALMS1P	cis	Thyroid	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
2	chr2:73822000-73838800	Weak transcription	Fetal Heart	heart
3	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
5	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:73826600-73839200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:73826800-73838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:73827000-73840600	Weak transcription	NHLF	lung
10	chr2:73827600-73839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:73829000-73839000	Weak transcription	NHDF-Ad	bronchial
13	chr2:73829000-73839400	Weak transcription	Placenta	Placenta
14	chr2:73829200-73840000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:73829600-73840200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:73829800-73839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:73829800-73840000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:73829800-73840000	Weak transcription	Gastric	stomach
20	chr2:73829800-73840400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:73830000-73840800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:73830400-73839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:73830400-73843600	Weak transcription	Aorta	Aorta
24	chr2:73830600-73838800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:73830600-73839000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:73830600-73839000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:73830600-73839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:73830600-73840000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:73830600-73841200	Weak transcription	Liver	Liver
30	chr2:73830600-73843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:73830600-73847600	Weak transcription	Spleen	Spleen
32	chr2:73830600-73854800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:73830800-73839200	Weak transcription	Osteobl	bone
34	chr2:73830800-73840800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:73831000-73842200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:73831200-73839600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:73831200-73841200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:73833800-73839200	Strong transcription	Fetal Brain Female	brain
39	chr2:73835400-73838800	Strong transcription	Fetal Intestine Small	intestine
40	chr2:73835400-73839000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:73835400-73839200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:73835600-73838800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:73835600-73838800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:73835600-73838800	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:73835800-73838800	Strong transcription	Brain Germinal Matrix	brain
46	chr2:73836000-73838800	Strong transcription	Fetal Stomach	stomach
47	chr2:73836200-73839200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:73836200-73839800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:73836400-73839600	Weak transcription	HSMM	muscle
50	chr2:73836400-73844200	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links