Variant report

Variant	rs1491985
Chromosome Location	chr3:49739507-49739508
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49739474..49741113-chr3:49755078..49756653,2	MCF-7	breast:
2	chr3:49737567..49739735-chr3:49821150..49823977,2	MCF-7	breast:
3	chr3:49735446..49741255-chr3:49749875..49755830,7	K562	blood:
4	chr3:49738438..49740011-chr3:49839951..49842563,2	K562	blood:
5	chr3:49735709..49738693-chr3:49739314..49743110,4	MCF-7	breast:
6	chr3:49717585..49720348-chr3:49739097..49740977,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction
ENSG00000176095	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1078341	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap]
rs11130217	0.94[CEU][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][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]
rs11720705	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637313	0.87[CEU][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs12715437	1.00[CEU][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap]
rs1463728	1.00[ASN][1000 genomes]
rs1491983	0.94[CEU][hapmap]
rs1532204	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs1586827	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs1799844	0.94[EUR][1000 genomes]
rs1996663	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2029591	0.94[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs2131108	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs2329021	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs28535523	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap]
rs35129566	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4241405	0.94[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs4855833	1.00[CEU][hapmap]
rs4855845	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs4855846	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs55997059	0.94[EUR][1000 genomes]
rs58339610	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59357103	0.92[EUR][1000 genomes]
rs59684465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61557789	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62260663	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260720	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260723	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs62262722	0.99[EUR][1000 genomes]
rs62262730	0.96[EUR][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap]
rs6790568	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs6804970	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620848	1.00[CEU][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621797	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7628207	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7637711	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7649428	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9829155	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9830730	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9835157	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9836756	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9849038	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9851651	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9870755	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870858	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9871024	1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[ASN][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1491985	AMT	cis	lung	GTEx
rs1491985	AMT	cis	Thyroid	GTEx
rs1491985	RNF123	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49727800-49740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49727800-49742200	Weak transcription	Small Intestine	intestine
3	chr3:49728000-49742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:49728000-49744400	Weak transcription	NH-A	brain
5	chr3:49728000-49748800	Weak transcription	A549	lung
6	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:49728600-49744800	Weak transcription	HMEC	breast
9	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:49729200-49749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:49729200-49750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
13	chr3:49729400-49750200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:49731800-49740800	Strong transcription	Fetal Stomach	stomach
15	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
16	chr3:49733000-49750200	Weak transcription	Psoas Muscle	Psoas
17	chr3:49734200-49746000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:49734200-49746000	Strong transcription	Thymus	Thymus
19	chr3:49734200-49746200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:49734400-49740400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:49734400-49740600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:49734400-49740800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:49734400-49741200	Strong transcription	Spleen	Spleen
24	chr3:49734400-49744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:49734400-49744000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:49734400-49744200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:49734400-49744400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:49734400-49744800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:49734400-49744800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:49734400-49745000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:49734400-49745200	Strong transcription	Fetal Brain Female	brain
32	chr3:49734400-49745400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:49734400-49745400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:49734400-49746000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:49734400-49746000	Strong transcription	Fetal Intestine Large	intestine
36	chr3:49734400-49746200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr3:49734400-49746200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr3:49734400-49746200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:49734400-49746400	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:49734400-49756000	Strong transcription	Liver	Liver
41	chr3:49734600-49740400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:49734600-49740600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:49734600-49741000	Strong transcription	Brain Angular Gyrus	brain
44	chr3:49734600-49741000	Strong transcription	Lung	lung
45	chr3:49734600-49741200	Strong transcription	Gastric	stomach
46	chr3:49734600-49744800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr3:49734600-49744800	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:49734600-49745000	Strong transcription	Esophagus	oesophagus
49	chr3:49734600-49745000	Strong transcription	Dnd41	blood
50	chr3:49734600-49745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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