Variant report

Variant	rs4713120
Chromosome Location	chr6:27721835-27721836
allele	A/C
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27218569..27220460-chr6:27719318..27721940,3	MCF-7	breast:
2	chr6:27516133..27518259-chr6:27720231..27723733,3	K562	blood:
3	chr6:27635070..27638218-chr6:27719785..27722837,4	K562	blood:
4	chr6:27444529..27447552-chr6:27720507..27722383,3	K562	blood:
5	chr6:27721516..27722337-chr6:27759817..27760598,2	K562	blood:
6	chr6:27720458..27723268-chr6:27776888..27778470,2	MCF-7	breast:
7	chr6:27480372..27481904-chr6:27721139..27723255,2	K562	blood:
8	chr6:27113190..27116258-chr6:27719531..27723256,5	K562	blood:
9	chr6:27694961..27696569-chr6:27720410..27723324,2	K562	blood:
10	chr6:27113421..27116397-chr6:27720119..27723593,4	K562	blood:
11	chr6:27520849..27522507-chr6:27719657..27722145,3	K562	blood:
12	chr6:27652463..27655224-chr6:27720018..27721922,3	K562	blood:
13	chr6:27124529..27126942-chr6:27720154..27721836,2	K562	blood:
14	chr6:27720750..27725347-chr6:27727186..27730834,4	MCF-7	breast:
15	chr6:27510934..27513659-chr6:27719612..27722020,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112812	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1022486	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs10946938	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10946940	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs200480	0.93[ASW][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.87[ASN][1000 genomes]
rs2056924	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2179096	0.84[AMR][1000 genomes]
rs2294480	0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2294481	0.86[JPT][hapmap]
rs57252182	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6456799	0.86[JPT][hapmap]
rs6915266	0.81[JPT][hapmap]
rs6921256	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs9295747	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9348772	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs9368527	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9380007	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393830	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs9393831	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs9468209	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468213	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4713120	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs4713120	ZSCAN23	cis	cerebellum	SCAN
rs4713120	ZKSCAN3	cis	cerebellum	SCAN
rs4713120	ZKSCAN3	cis	parietal	SCAN
rs4713120	BTN3A3	cis	cerebellum	SCAN
rs4713120	AL022393.7	cis	Muscle Skeletal	GTEx
rs4713120	BTN3A3	cis	parietal	SCAN
rs4713120	HIST1H3I	cis	cerebellum	SCAN
rs4713120	ZNF323	cis	parietal	SCAN
rs4713120	ZSCAN16	cis	parietal	SCAN
rs4713120	ZNF323	cis	cerebellum	SCAN
rs4713120	ABT1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27719800-27722200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:27719800-27722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr6:27719800-27722400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:27720000-27722000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:27720000-27722000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:27720000-27722000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:27720000-27722200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr6:27720000-27722200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:27720000-27722200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:27720000-27722200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:27720000-27722200	Active TSS	Brain Hippocampus Middle	brain
12	chr6:27720000-27722200	Active TSS	Thymus	Thymus
13	chr6:27720000-27722400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr6:27720000-27722400	Active TSS	Brain Anterior Caudate	brain
15	chr6:27720000-27722400	Active TSS	Brain Germinal Matrix	brain
16	chr6:27720000-27722600	Active TSS	Fetal Kidney	kidney
17	chr6:27720000-27723000	Active TSS	A549	lung
18	chr6:27720200-27722000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:27720200-27722000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:27720200-27722000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:27720200-27722000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:27720200-27722000	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:27720200-27722000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr6:27720200-27722000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:27720200-27722000	Active TSS	Colon Smooth Muscle	Colon
26	chr6:27720200-27722000	Active TSS	Duodenum Mucosa	Duodenum
27	chr6:27720200-27722000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:27720200-27722000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr6:27720200-27722000	Active TSS	Fetal Muscle Trunk	muscle
30	chr6:27720200-27722000	Active TSS	Fetal Stomach	stomach
31	chr6:27720200-27722000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr6:27720200-27722000	Active TSS	GM12878-XiMat	blood
33	chr6:27720200-27722000	Active TSS	NHEK	skin
34	chr6:27720200-27722200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:27720200-27722200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:27720200-27722200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:27720200-27722200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:27720200-27722200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:27720200-27722200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:27720200-27722200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:27720200-27722200	Active TSS	Brain Substantia Nigra	brain
42	chr6:27720200-27722200	Active TSS	Colonic Mucosa	Colon
43	chr6:27720200-27722200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:27720200-27722200	Active TSS	Fetal Lung	lung
45	chr6:27720200-27722200	Active TSS	Placenta	Placenta
46	chr6:27720200-27722200	Active TSS	Left Ventricle	heart
47	chr6:27720200-27722200	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr6:27720200-27722200	Active TSS	Stomach Smooth Muscle	stomach
49	chr6:27720200-27722200	Active TSS	Hela-S3	cervix
50	chr6:27720200-27722200	Active TSS	HMEC	breast

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