Variant report

Variant	rs7620024
Chromosome Location	chr3:49451691-49451692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49451385-49452540	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49449662..49452069-chr3:49709335..49712259,2	K562	blood:
2	chr3:49375112..49379681-chr3:49446166..49452291,17	K562	blood:
3	chr3:49449761..49451817-chr3:49454782..49457438,2	MCF-7	breast:
4	chr3:49448910..49451821-chr3:49459047..49464749,5	MCF-7	breast:
5	chr3:49449931..49451765-chr3:49466713..49468674,2	MCF-7	breast:
6	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:

No data

Variant related genes	Relation type
RHOA	TF binding region
ENSG00000114316	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000145020	Chromatin interaction
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1009051	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10155014	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.84[EUR][1000 genomes]
rs1106620	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130190	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11710434	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11715060	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719762	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11720657	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11923032	0.83[AMR][1000 genomes]
rs11928090	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	0.84[EUR][1000 genomes]
rs13096474	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1464569	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982861	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2177268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2312462	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329025	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3448	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3866330	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870339	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870341	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905330	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4052546	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241407	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855837	0.81[EUR][1000 genomes]
rs4855853	0.82[EUR][1000 genomes]
rs4855858	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855869	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4955413	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4955417	1.00[ASN][1000 genomes]
rs4955424	0.89[EUR][1000 genomes]
rs4955425	0.88[EUR][1000 genomes]
rs4955430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56127630	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57273516	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259933	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62259943	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62259944	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62259947	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62261183	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62261249	0.83[EUR][1000 genomes]
rs6446262	0.91[EUR][1000 genomes]
rs6446275	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6769744	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775069	0.90[EUR][1000 genomes]
rs6778080	0.81[AMR][1000 genomes]
rs6783003	0.89[EUR][1000 genomes]
rs6784203	0.89[EUR][1000 genomes]
rs6785045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6790105	0.81[EUR][1000 genomes]
rs6796147	0.87[EUR][1000 genomes]
rs6805609	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809204	0.86[EUR][1000 genomes]
rs72934271	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73088137	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355800	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7374731	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7613491	0.90[EUR][1000 genomes]
rs7619789	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622786	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7625857	0.81[EUR][1000 genomes]
rs7638750	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7644148	0.86[EUR][1000 genomes]
rs7647973	0.90[EUR][1000 genomes]
rs7648995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7651372	0.87[EUR][1000 genomes]
rs8897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs940045	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654010	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs974495	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757181	0.82[EUR][1000 genomes]
rs9809237	0.86[EUR][1000 genomes]
rs9812360	0.84[EUR][1000 genomes]
rs9817807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9842132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9860055	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9860285	0.83[EUR][1000 genomes]
rs9861027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9862534	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9881860	0.81[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
rs7620024	WDR6	cis	Muscle Skeletal	GTEx
rs7620024	AMT	cis	Muscle Skeletal	GTEx
rs7620024	AMT	cis	Esophagus Muscularis	GTEx
rs7620024	AMT	cis	Whole Blood	GTEx
rs7620024	NICN1	cis	Thyroid	GTEx
rs7620024	WDR6	cis	Esophagus Muscularis	GTEx
rs7620024	NICN1-AS1	cis	Thyroid	GTEx
rs7620024	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs7620024	AMT	cis	Esophagus Mucosa	GTEx
rs7620024	AMT	cis	Adipose Subcutaneous	GTEx
rs7620024	AMT	cis	Artery Aorta	GTEx
rs7620024	AMT	cis	Artery Tibial	GTEx
rs7620024	AMT	cis	Thyroid	GTEx
rs7620024	AMT	cis	Nerve Tibial	GTEx
rs7620024	WDR6	cis	Nerve Tibial	GTEx
rs7620024	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs7620024	AMT	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49450400-49459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49450400-49459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49450600-49452400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:49450600-49453200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:49450600-49453800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:49450600-49453800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:49450600-49454400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:49450600-49454600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:49450600-49459000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:49450800-49452000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:49450800-49452000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49450800-49452000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:49450800-49452200	Weak transcription	Aorta	Aorta
14	chr3:49450800-49452400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:49450800-49452600	Genic enhancers	Primary B cells from cord blood	blood
16	chr3:49450800-49452600	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr3:49450800-49452600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:49450800-49453200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:49450800-49453400	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr3:49450800-49453600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:49450800-49453800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:49450800-49454000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:49450800-49454200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:49450800-49454400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:49450800-49455400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:49450800-49457800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:49450800-49459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:49450800-49459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:49450800-49459200	Genic enhancers	Placenta	Placenta
30	chr3:49451000-49451800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:49451000-49452000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:49451000-49452000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:49451000-49453200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr3:49451000-49453600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:49451000-49454400	Weak transcription	Fetal Kidney	kidney
36	chr3:49451000-49458000	Weak transcription	Small Intestine	intestine
37	chr3:49451200-49451800	Weak transcription	Spleen	Spleen
38	chr3:49451200-49452000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:49451200-49452000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:49451200-49452000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:49451200-49452000	Weak transcription	Brain Germinal Matrix	brain
42	chr3:49451200-49452000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:49451200-49452000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:49451200-49452000	Weak transcription	Thymus	Thymus
45	chr3:49451200-49452000	Weak transcription	A549	lung
46	chr3:49451200-49452000	Weak transcription	HMEC	breast
47	chr3:49451200-49452000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:49451200-49452000	Weak transcription	NHEK	skin
49	chr3:49451200-49452200	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:49451200-49452200	Weak transcription	Esophagus	oesophagus

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