Variant report

Variant	rs2329025
Chromosome Location	chr3:49496263-49496264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49494808..49501210-chr3:49505386..49509341,14	MCF-7	breast:
2	chr3:49493044..49494602-chr3:49495069..49497320,2	K562	blood:
3	chr3:49492642..49496554-chr3:49506266..49510118,5	MCF-7	breast:
4	chr3:49493317..49496589-chr3:49498122..49502213,4	K562	blood:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1009051	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10155014	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1106620	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11130190	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11715060	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719762	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11923032	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11928090	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096474	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1464569	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2177268	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2312462	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3866330	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855837	0.85[EUR][1000 genomes]
rs4855853	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855858	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4955417	1.00[ASN][1000 genomes]
rs4955424	0.82[EUR][1000 genomes]
rs4955425	0.83[EUR][1000 genomes]
rs4955430	0.85[EUR][1000 genomes]
rs56127630	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56324858	0.82[EUR][1000 genomes]
rs57273516	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62259943	0.87[EUR][1000 genomes]
rs62259944	0.84[EUR][1000 genomes]
rs62259947	0.89[EUR][1000 genomes]
rs62261183	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62261249	0.89[EUR][1000 genomes]
rs6446262	0.84[EUR][1000 genomes]
rs6446275	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6769744	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775069	0.85[EUR][1000 genomes]
rs6783003	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6784203	0.83[EUR][1000 genomes]
rs6785045	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6796147	0.82[EUR][1000 genomes]
rs6805609	0.92[EUR][1000 genomes]
rs6809204	0.82[EUR][1000 genomes]
rs72934271	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088137	0.90[EUR][1000 genomes]
rs7355800	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7374731	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7613491	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7619789	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620024	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7625857	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7638750	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7644148	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7647973	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7648995	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7651372	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7653505	0.90[AFR][1000 genomes]
rs8897	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs940045	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs974495	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757181	0.85[AFR][1000 genomes]
rs9809237	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9817807	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9842132	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9860055	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9861027	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9862534	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2329025	AMT	cis	lung	GTEx
rs2329025	AMT	cis	Muscle Skeletal	GTEx
rs2329025	WDR6	cis	lung	GTEx
rs2329025	AMT	cis	Nerve Tibial	GTEx
rs2329025	AMT	cis	Whole Blood	GTEx
rs2329025	WDR6	cis	Esophagus Muscularis	GTEx
rs2329025	AMT	cis	Artery Tibial	GTEx
rs2329025	AMT	cis	Thyroid	GTEx
rs2329025	AMT	cis	Artery Aorta	GTEx
rs2329025	AMT	cis	Esophagus Muscularis	GTEx
rs2329025	NICN1-AS1	cis	Thyroid	GTEx
rs2329025	WDR6	cis	Nerve Tibial	GTEx
rs2329025	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs2329025	AMT	cis	Adipose Subcutaneous	GTEx
rs2329025	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs2329025	NICN1	cis	Thyroid	GTEx
rs2329025	AMT	cis	Esophagus Mucosa	GTEx
rs2329025	WDR6	cis	Muscle Skeletal	GTEx
rs2329025	AMT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49482000-49498200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:49486600-49498600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
4	chr3:49491800-49506200	Enhancers	Placenta	Placenta
5	chr3:49492600-49498000	Weak transcription	Stomach Mucosa	stomach
6	chr3:49492800-49496400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:49492800-49496400	Weak transcription	Fetal Kidney	kidney
8	chr3:49492800-49496400	Weak transcription	Lung	lung
9	chr3:49492800-49498800	Weak transcription	Right Atrium	heart
10	chr3:49492800-49499200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:49493000-49496400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:49493000-49496400	Weak transcription	Ovary	ovary
13	chr3:49493000-49496600	Weak transcription	Gastric	stomach
14	chr3:49493000-49498400	Weak transcription	Esophagus	oesophagus
15	chr3:49493200-49496400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:49493200-49498600	Weak transcription	Spleen	Spleen
17	chr3:49493400-49496400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:49493400-49498800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:49493600-49497800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:49493800-49496400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:49494000-49496400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:49494000-49498600	Weak transcription	Left Ventricle	heart
23	chr3:49494000-49498800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:49494000-49498800	Weak transcription	Psoas Muscle	Psoas
25	chr3:49494200-49496800	Weak transcription	Fetal Heart	heart
26	chr3:49494200-49497800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:49494200-49497800	Weak transcription	HMEC	breast
28	chr3:49494200-49498200	Weak transcription	NHEK	skin
29	chr3:49494200-49498600	Weak transcription	NHLF	lung
30	chr3:49494200-49499000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:49494200-49499000	Weak transcription	Osteobl	bone
32	chr3:49494600-49501800	Enhancers	Fetal Muscle Trunk	muscle
33	chr3:49494800-49497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:49494800-49498800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:49494800-49498800	Weak transcription	Right Ventricle	heart
36	chr3:49495000-49496400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:49495000-49496600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:49495000-49496800	Weak transcription	A549	lung
39	chr3:49495000-49498600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:49495000-49498800	Weak transcription	NHDF-Ad	bronchial
41	chr3:49496000-49500000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:49496000-49501400	Enhancers	Pancreas	Pancrea
43	chr3:49496200-49496400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:49496200-49496400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:49496200-49496400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:49496200-49496600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:49496200-49497000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:49496200-49498000	Enhancers	Fetal Stomach	stomach
49	chr3:49496200-49498200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr3:49496200-49498200	Flanking Active TSS	HepG2	liver

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