Variant report

Variant	rs3800489
Chromosome Location	chr6:64411814-64411815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:64411797-64411828	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
PHF3	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1029091	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10943958	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10944026	0.91[ASN][1000 genomes]
rs13197043	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13199206	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13199805	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13208965	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13216525	0.91[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1412864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1412865	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2627797	0.81[YRI][hapmap]
rs3800490	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4142266	0.82[ASN][1000 genomes]
rs4351235	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4634434	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4710256	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4710257	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4710436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4710439	0.91[ASN][1000 genomes]
rs58429651	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs756274	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs7762059	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7764184	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830674	chr6:64355412-64535801	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1022376	chr6:64386826-64445195	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800489	LGSN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64347000-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:64354000-64421200	Weak transcription	Gastric	stomach
3	chr6:64370800-64413400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:64374200-64414600	Weak transcription	HMEC	breast
5	chr6:64384600-64414400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:64387200-64421000	Weak transcription	Aorta	Aorta
7	chr6:64387400-64419400	Weak transcription	Fetal Heart	heart
8	chr6:64387600-64421000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:64387600-64423400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:64388000-64412800	Weak transcription	Lung	lung
11	chr6:64390000-64417600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:64392200-64422400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:64392800-64425200	Weak transcription	NHEK	skin
14	chr6:64393200-64417600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:64393400-64423400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:64394600-64414000	Weak transcription	NHLF	lung
17	chr6:64394800-64413200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:64394800-64413200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:64394800-64414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:64395000-64413200	Weak transcription	NH-A	brain
21	chr6:64395000-64414000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:64395000-64414000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:64395000-64414800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:64395200-64413600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:64395400-64420200	Weak transcription	Fetal Brain Male	brain
26	chr6:64395800-64413600	Weak transcription	Brain Anterior Caudate	brain
27	chr6:64395800-64420200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:64396000-64413600	Weak transcription	HSMMtube	muscle
29	chr6:64396200-64414000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:64397400-64422400	Weak transcription	Pancreas	Pancrea
31	chr6:64399200-64418600	Weak transcription	A549	lung
32	chr6:64401000-64426400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:64402000-64419200	Weak transcription	Brain Substantia Nigra	brain
34	chr6:64403400-64414000	Weak transcription	Esophagus	oesophagus
35	chr6:64404000-64424600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr6:64404200-64417400	Strong transcription	Fetal Lung	lung
37	chr6:64404200-64423600	Strong transcription	Dnd41	blood
38	chr6:64404200-64423800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr6:64404200-64424200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:64404200-64424600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:64404200-64424600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:64404200-64426600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:64404400-64417600	Strong transcription	HepG2	liver
44	chr6:64404400-64424200	Strong transcription	Fetal Thymus	thymus
45	chr6:64404400-64424800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:64404400-64425000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:64404400-64426800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:64404600-64412000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:64404800-64420600	Weak transcription	Small Intestine	intestine
50	chr6:64404800-64424200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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