Variant report

Variant	rs3804778
Chromosome Location	chr3:101294572-101294573
allele	A/G
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	chr3:101293011..101294602-chr3:101404209..101407193,2	K562	blood:
2	chr3:101293909..101295477-chr3:101345124..101347411,2	K562	blood:
3	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
4	chr3:101291104..101295547-chr3:101393750..101397705,12	MCF-7	breast:
5	chr3:101291780..101294720-chr3:101394004..101396565,4	K562	blood:
6	chr3:101293308..101296113-chr3:101394030..101397396,3	MCF-7	breast:
7	chr3:101290641..101295184-chr3:101404268..101406806,5	MCF-7	breast:
8	chr3:101291201..101295304-chr3:101402286..101407928,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000212319	Chromatin interaction
ENSG00000114391	Chromatin interaction
ENSG00000256628	Chromatin interaction
ENSG00000066422	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1031710	0.90[JPT][hapmap]
rs10936707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708616	0.90[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs11708845	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710016	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap]
rs11710533	0.81[ASN][1000 genomes]
rs11711808	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs11712748	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11715368	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720560	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11914318	0.95[JPT][hapmap]
rs11919389	0.90[JPT][hapmap]
rs11923273	0.84[ASN][1000 genomes]
rs12638137	0.81[EUR][1000 genomes]
rs12638796	0.85[EUR][1000 genomes]
rs12639028	0.82[ASN][1000 genomes]
rs13059470	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs13065944	0.90[JPT][hapmap]
rs13066768	0.90[JPT][hapmap]
rs13069443	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs13081846	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17345528	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345786	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17411983	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17508319	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288272	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3094296	0.95[JPT][hapmap]
rs3094297	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs34376498	0.90[JPT][hapmap]
rs35117343	0.90[JPT][hapmap]
rs35850993	0.90[JPT][hapmap]
rs3762729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806653	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3806654	0.95[JPT][hapmap]
rs55641278	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55710435	0.85[EUR][1000 genomes]
rs57880921	0.85[EUR][1000 genomes]
rs58835747	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58907984	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59359251	0.81[EUR][1000 genomes]
rs60837174	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6791964	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72944107	0.85[EUR][1000 genomes]
rs72946021	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73863360	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629753	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7641261	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651721	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs9830943	0.90[JPT][hapmap]
rs997739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3804778	NIT2	cis	parietal	SCAN
rs3804778	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101291400-101294800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:101291600-101295000	Active TSS	K562	blood
3	chr3:101292000-101294600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:101292000-101294800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr3:101292000-101294800	Active TSS	Right Ventricle	heart
6	chr3:101292000-101295000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:101292000-101295200	Active TSS	Psoas Muscle	Psoas
8	chr3:101292200-101294600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:101292200-101295000	Active TSS	Right Atrium	heart
10	chr3:101292400-101294600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:101292400-101294600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:101292400-101294600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:101292400-101294600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:101292400-101294600	Active TSS	NHDF-Ad	bronchial
15	chr3:101292400-101294800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:101292400-101294800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:101292400-101294800	Active TSS	GM12878-XiMat	blood
18	chr3:101292400-101295000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:101292400-101295000	Active TSS	HSMMtube	muscle
20	chr3:101292600-101294600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:101292600-101294600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:101292600-101294600	Active TSS	Fetal Kidney	kidney
23	chr3:101292600-101294600	Active TSS	NHEK	skin
24	chr3:101292600-101294600	Active TSS	NHLF	lung
25	chr3:101292600-101294800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:101292600-101295000	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr3:101292600-101295000	Active TSS	A549	lung
28	chr3:101292600-101295000	Active TSS	NH-A	brain
29	chr3:101292600-101295200	Active TSS	HMEC	breast
30	chr3:101293400-101294600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr3:101293600-101294600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:101293600-101294600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:101293600-101294800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr3:101293600-101294800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:101293600-101294800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:101293600-101294800	Active TSS	Brain Germinal Matrix	brain
37	chr3:101293600-101294800	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr3:101293600-101294800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr3:101293600-101295000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:101293800-101294600	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr3:101293800-101294600	Flanking Active TSS	Liver	Liver
42	chr3:101293800-101294800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr3:101293800-101294800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:101293800-101295000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:101293800-101295000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:101293800-101295600	Weak transcription	Spleen	Spleen
47	chr3:101294000-101294600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:101294000-101294600	Active TSS	HepG2	liver
49	chr3:101294000-101294800	Enhancers	Primary B cells from peripheral blood	blood
50	chr3:101294000-101294800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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