Variant report

Variant	rs3789362
Chromosome Location	chr1:180951692-180951693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180940551..180943228-chr1:180950361..180952940,2	MCF-7	breast:
2	chr1:180949324..180951935-chr1:180953444..180956382,3	K562	blood:
3	chr1:180943968..180947141-chr1:180950568..180953802,3	MCF-7	breast:
4	chr1:180951063..180953741-chr1:181057832..181059498,2	MCF-7	breast:
5	chr1:180949324..180952994-chr1:180953444..180956382,4	K562	blood:
6	chr1:180948321..180949844-chr1:180950401..180952045,2	K562	blood:
7	chr1:180950797..180952417-chr1:181056413..181058778,2	K562	blood:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000234237	Chromatin interaction
ENSG00000243155	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1044595	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753232	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586493	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12744212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754041	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2331903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3747957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][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]
rs3789364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4111520	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4495657	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4652548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs59145927	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6665134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516739	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543927	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7556005	0.88[JPT][hapmap]
rs883859	0.82[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
2	chr1:180929000-180956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:180939200-180954400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:180939200-180965600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:180943000-180957400	Weak transcription	Fetal Heart	heart
8	chr1:180943600-180955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180943600-180972000	Weak transcription	Psoas Muscle	Psoas
10	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:180944400-180962600	Strong transcription	Osteobl	bone
12	chr1:180944600-180957600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:180944800-180952600	Strong transcription	A549	lung
14	chr1:180944800-180970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:180945800-180956200	Weak transcription	Colonic Mucosa	Colon
18	chr1:180946000-180952200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:180946000-180953800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:180946200-180954600	Weak transcription	NHLF	lung
21	chr1:180946600-180952000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:180946600-180953400	Weak transcription	HUVEC	blood vessel
23	chr1:180946600-180954400	Weak transcription	Ovary	ovary
24	chr1:180946600-180955200	Weak transcription	Esophagus	oesophagus
25	chr1:180946800-180953400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:180946800-180955200	Weak transcription	Pancreas	Pancrea
27	chr1:180947200-180956000	Weak transcription	NH-A	brain
28	chr1:180947800-180954600	Weak transcription	Aorta	Aorta
29	chr1:180948200-180959400	Weak transcription	Stomach Mucosa	stomach
30	chr1:180948600-180952200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:180948600-180961400	Strong transcription	Fetal Intestine Large	intestine
32	chr1:180948800-180952600	Genic enhancers	Fetal Thymus	thymus
33	chr1:180948800-180959800	Strong transcription	Left Ventricle	heart
34	chr1:180948800-180961000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:180949000-180962400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:180949000-180962600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:180949200-180952600	Strong transcription	HSMMtube	muscle
38	chr1:180949400-180951800	Strong transcription	Brain Germinal Matrix	brain
39	chr1:180949400-180952600	Strong transcription	HSMM	muscle
40	chr1:180949400-180957400	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:180949400-180963800	Strong transcription	Liver	Liver
42	chr1:180949800-180952200	Enhancers	Thymus	Thymus
43	chr1:180949800-180952800	Enhancers	Brain Cingulate Gyrus	brain
44	chr1:180949800-180962600	Strong transcription	Adipose Nuclei	Adipose
45	chr1:180949800-180962600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:180949800-180963800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:180949800-180966200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:180950000-180951800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:180950000-180952000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:180950000-180952000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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