Variant report

Variant	rs1412865
Chromosome Location	chr6:64377539-64377540
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:64344529..64346659-chr6:64375006..64377744,2	K562	blood:
2	chr6:64344821..64347444-chr6:64375995..64378797,3	MCF-7	breast:
3	chr6:64375038..64377882-chr6:64378142..64379826,2	K562	blood:
4	chr6:64369626..64372438-chr6:64376058..64378974,3	K562	blood:
5	chr6:64347337..64350491-chr6:64374830..64379357,4	K562	blood:
6	chr6:64376354..64377916-chr6:64381170..64383377,2	MCF-7	breast:
7	chr6:64281916..64284591-chr6:64376493..64379119,2	MCF-7	breast:
8	chr6:64375915..64378129-chr6:64385885..64387947,2	MCF-7	breast:
9	chr6:64348462..64350491-chr6:64377129..64380030,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000118482	Chromatin interaction
ENSG00000112245	Chromatin interaction
ENSG00000266680	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1029091	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10943958	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10944026	0.81[ASN][1000 genomes]
rs13199206	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13199805	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13208965	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1412864	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800489	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3800490	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351235	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4634434	0.85[ASN][1000 genomes]
rs4710256	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4710257	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4710436	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4710439	0.81[ASN][1000 genomes]
rs58429651	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7764184	0.85[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1412865	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64347000-64383200	Weak transcription	Esophagus	oesophagus
2	chr6:64347000-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:64347600-64381000	Weak transcription	Fetal Thymus	thymus
4	chr6:64347800-64386400	Weak transcription	Colonic Mucosa	Colon
5	chr6:64350200-64381200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:64350200-64382800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:64351200-64385000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:64351200-64405000	Weak transcription	Thymus	Thymus
9	chr6:64354000-64421200	Weak transcription	Gastric	stomach
10	chr6:64354200-64383600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:64355200-64381600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:64357400-64381200	Weak transcription	Dnd41	blood
13	chr6:64357800-64393400	Weak transcription	Placenta	Placenta
14	chr6:64358400-64382800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:64363200-64382800	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:64365200-64387000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:64365400-64386400	Weak transcription	Spleen	Spleen
18	chr6:64365800-64409400	Weak transcription	Fetal Stomach	stomach
19	chr6:64366600-64382400	Weak transcription	Fetal Lung	lung
20	chr6:64368000-64380600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:64368000-64381800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:64370800-64378000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:64370800-64383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:64370800-64383400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:64370800-64395000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:64370800-64413400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:64371000-64381200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:64371000-64381200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:64371000-64394200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:64371000-64409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:64371400-64383200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:64371400-64383200	Weak transcription	Liver	Liver
33	chr6:64373600-64382600	Weak transcription	Ovary	ovary
34	chr6:64373800-64380600	Weak transcription	HepG2	liver
35	chr6:64373800-64383400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:64373800-64384600	Weak transcription	Adipose Nuclei	Adipose
37	chr6:64373800-64386400	Weak transcription	Pancreas	Pancrea
38	chr6:64373800-64394200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:64373800-64394600	Weak transcription	HSMMtube	muscle
40	chr6:64373800-64394800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:64374000-64381200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:64374000-64384400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:64374000-64384600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:64374000-64384800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:64374000-64386200	Weak transcription	NHDF-Ad	bronchial
46	chr6:64374000-64387200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:64374000-64391600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:64374200-64378000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:64374200-64378000	Weak transcription	Small Intestine	intestine
50	chr6:64374200-64379200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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