Variant report

Variant	rs1106620
Chromosome Location	chr3:49500414-49500415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49493317..49496589-chr3:49498122..49502213,4	K562	blood:
2	chr3:49494808..49501210-chr3:49505386..49509341,14	MCF-7	breast:
3	chr3:49025870..49028147-chr3:49498822..49500854,2	K562	blood:
4	chr3:49492720..49494835-chr3:49497709..49500473,4	MCF-7	breast:
5	chr3:49496719..49502585-chr3:49503472..49509213,13	MCF-7	breast:
6	chr3:49054424..49056123-chr3:49498434..49500923,2	K562	blood:
7	chr3:49452077..49454427-chr3:49496570..49500540,3	MCF-7	breast:
8	chr3:49499007..49500674-chr3:49711634..49713194,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000178467	Chromatin interaction
ENSG00000223343	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000201301	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1009051	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10155014	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865956	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130190	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130207	0.81[AFR][1000 genomes]
rs11130208	0.85[AFR][1000 genomes]
rs11715060	0.85[EUR][1000 genomes]
rs11719762	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11720657	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11923032	0.83[EUR][1000 genomes]
rs11928090	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12583	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096474	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13322887	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1464569	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1532204	0.85[AFR][1000 genomes]
rs1982861	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2140270	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2177268	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2312462	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2329025	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3448	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3866330	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3870339	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3870341	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3905330	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4052546	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4241407	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4855837	0.86[EUR][1000 genomes]
rs4855853	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855858	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855869	0.91[EUR][1000 genomes]
rs4955413	0.80[EUR][1000 genomes]
rs4955424	0.83[EUR][1000 genomes]
rs4955425	0.82[EUR][1000 genomes]
rs4955430	0.86[EUR][1000 genomes]
rs56127630	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56324858	0.83[EUR][1000 genomes]
rs57273516	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62259933	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62259943	0.88[EUR][1000 genomes]
rs62259944	0.85[EUR][1000 genomes]
rs62259947	0.89[EUR][1000 genomes]
rs62261183	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62261249	0.88[EUR][1000 genomes]
rs6446262	0.85[EUR][1000 genomes]
rs6446275	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6769744	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6775069	0.84[EUR][1000 genomes]
rs6783003	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6784203	0.83[EUR][1000 genomes]
rs6785045	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6796147	0.81[EUR][1000 genomes]
rs6797299	0.85[AFR][1000 genomes]
rs6805609	0.93[EUR][1000 genomes]
rs6809204	0.83[EUR][1000 genomes]
rs72934271	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088137	0.91[EUR][1000 genomes]
rs7355800	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7374731	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7613491	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7619789	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7620024	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7622786	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7625857	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7638750	0.85[EUR][1000 genomes]
rs7644148	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7647973	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7648995	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7651372	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8897	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs940045	0.90[EUR][1000 genomes]
rs9654010	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs974495	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9809237	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9817807	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9842132	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9860055	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9861027	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9862534	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9871024	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1106620	NICN1	cis	Thyroid	GTEx
rs1106620	AMT	cis	Nerve Tibial	GTEx
rs1106620	NICN1-AS1	cis	Thyroid	GTEx
rs1106620	AMT	cis	lung	GTEx
rs1106620	AMT	cis	Esophagus Mucosa	GTEx
rs1106620	AMT	cis	Thyroid	GTEx
rs1106620	AMT	cis	Whole Blood	GTEx
rs1106620	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs1106620	WDR6	cis	Esophagus Muscularis	GTEx
rs1106620	WDR6	cis	Muscle Skeletal	GTEx
rs1106620	AMT	cis	Artery Aorta	GTEx
rs1106620	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs1106620	AMT	cis	Artery Tibial	GTEx
rs1106620	AMT	cis	Adipose Subcutaneous	GTEx
rs1106620	WDR6	cis	Nerve Tibial	GTEx
rs1106620	AMT	cis	Esophagus Muscularis	GTEx
rs1106620	AMT	cis	Muscle Skeletal	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49490600-49506600	Enhancers	Fetal Muscle Leg	muscle
2	chr3:49491800-49506200	Enhancers	Placenta	Placenta
3	chr3:49494600-49501800	Enhancers	Fetal Muscle Trunk	muscle
4	chr3:49496000-49501400	Enhancers	Pancreas	Pancrea
5	chr3:49496200-49501200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:49496200-49501200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:49496200-49501200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:49496400-49501200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:49496400-49501400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:49497400-49506400	Weak transcription	Brain Germinal Matrix	brain
11	chr3:49498000-49506000	Weak transcription	Fetal Stomach	stomach
12	chr3:49499000-49501000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:49499400-49500800	Weak transcription	Ovary	ovary
14	chr3:49499400-49501600	Enhancers	HepG2	liver
15	chr3:49499600-49501600	Enhancers	Hela-S3	cervix
16	chr3:49499600-49503000	Weak transcription	Colonic Mucosa	Colon
17	chr3:49499600-49503000	Weak transcription	Right Atrium	heart
18	chr3:49499600-49503000	Weak transcription	Spleen	Spleen
19	chr3:49499600-49503200	Weak transcription	Esophagus	oesophagus
20	chr3:49499600-49503200	Weak transcription	Lung	lung
21	chr3:49499600-49503200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:49499600-49506600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:49499800-49502600	Weak transcription	Fetal Heart	heart
24	chr3:49499800-49503000	Weak transcription	Right Ventricle	heart
25	chr3:49499800-49503000	Weak transcription	HMEC	breast
26	chr3:49500000-49501000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:49500000-49502400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:49500000-49502400	Weak transcription	NHEK	skin
29	chr3:49500000-49502600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:49500000-49502800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:49500000-49502800	Weak transcription	Fetal Intestine Large	intestine
32	chr3:49500000-49502800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:49500000-49503000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:49500000-49503000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:49500000-49503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:49500000-49503000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:49500000-49503000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:49500000-49503000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:49500000-49503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:49500000-49503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:49500000-49503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:49500000-49503000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:49500000-49503000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:49500000-49503000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:49500000-49503000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:49500000-49503000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:49500000-49503000	Weak transcription	Gastric	stomach
48	chr3:49500000-49503000	Weak transcription	Left Ventricle	heart
49	chr3:49500000-49503000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:49500000-49503000	Weak transcription	Rectal Mucosa Donor 31	rectum

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