Variant report

Variant	rs67859638
Chromosome Location	chr6:27357978-27357979
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:9)
LncRNA
region (count:1)
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	chr6:27113785..27116304-chr6:27356399..27358052,2	K562	blood:
2	chr6:27356277..27359093-chr6:27439899..27443040,4	MCF-7	breast:
3	chr6:27114804..27117756-chr6:27356552..27360776,4	K562	blood:
4	chr6:27357105..27360959-chr6:27363374..27365305,4	K562	blood:
5	chr6:27356362..27358956-chr6:27773296..27775539,3	K562	blood:
6	chr6:27357897..27360026-chr6:27439101..27441512,2	K562	blood:
7	chr6:27342371..27343890-chr6:27355850..27358027,2	K562	blood:
8	chr6:27356907..27359078-chr6:27397692..27399728,2	K562	blood:
9	chr6:27291445..27294642-chr6:27355178..27358043,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS16-2	chr6:27357718-27358702	NONHSAT108380

No data

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10484399	0.83[EUR][1000 genomes]
rs13191227	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13191474	0.91[EUR][1000 genomes]
rs13195040	0.91[EUR][1000 genomes]
rs13195636	0.85[EUR][1000 genomes]
rs13196692	0.98[EUR][1000 genomes]
rs13207082	0.81[AMR][1000 genomes]
rs13207689	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13209332	0.85[EUR][1000 genomes]
rs13212562	0.82[EUR][1000 genomes]
rs13218537	0.98[EUR][1000 genomes]
rs28360634	0.96[EUR][1000 genomes]
rs34071253	0.96[EUR][1000 genomes]
rs34196306	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34332556	0.98[EUR][1000 genomes]
rs34573979	0.89[EUR][1000 genomes]
rs34613987	0.82[EUR][1000 genomes]
rs34864796	0.82[EUR][1000 genomes]
rs34953377	0.98[EUR][1000 genomes]
rs34965299	0.85[EUR][1000 genomes]
rs35120058	0.98[EUR][1000 genomes]
rs35716472	0.96[EUR][1000 genomes]
rs35768595	1.00[AFR][1000 genomes]
rs35848276	0.85[EUR][1000 genomes]
rs35984974	0.96[EUR][1000 genomes]
rs41269265	0.91[EUR][1000 genomes]
rs56114371	0.81[AMR][1000 genomes]
rs56401801	0.90[EUR][1000 genomes]
rs58616630	0.89[EUR][1000 genomes]
rs66785117	0.85[EUR][1000 genomes]
rs66841633	0.98[EUR][1000 genomes]
rs67240003	0.82[EUR][1000 genomes]
rs6904596	0.82[EUR][1000 genomes]
rs6918792	0.81[EUR][1000 genomes]
rs71537559	0.92[EUR][1000 genomes]
rs72839445	0.90[AMR][1000 genomes]
rs72839477	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7749305	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs67859638	BTN3A2	cis	Esophagus Mucosa	GTEx
rs67859638	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs67859638	BTN3A2	cis	Nerve Tibial	GTEx
rs67859638	BTN3A2	cis	lung	GTEx
rs67859638	BTN3A2	cis	Thyroid	GTEx
rs67859638	BTN3A2	cis	Whole Blood	GTEx
rs67859638	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs67859638	BTN3A2	cis	Artery Tibial	GTEx
rs67859638	BTN3A2	cis	Heart Left Ventricle	GTEx
rs67859638	BTN3A2	cis	Muscle Skeletal	GTEx
rs67859638	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27355600-27358400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:27355800-27358000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27355800-27358000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:27356200-27358000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr6:27356800-27358000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:27357000-27358000	Flanking Active TSS	Dnd41	blood
7	chr6:27357200-27358200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:27357200-27362200	Weak transcription	Aorta	Aorta
9	chr6:27357200-27366600	Weak transcription	Left Ventricle	heart
10	chr6:27357400-27358200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:27357400-27361600	Weak transcription	Colonic Mucosa	Colon
12	chr6:27357400-27363000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:27357400-27363000	Weak transcription	Right Atrium	heart
14	chr6:27357400-27364200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:27357400-27364800	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:27357400-27364800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:27357400-27365000	Weak transcription	Fetal Lung	lung
18	chr6:27357400-27366000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:27357400-27367000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:27357400-27367200	Weak transcription	Brain Substantia Nigra	brain
21	chr6:27357400-27367800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:27357400-27368000	Weak transcription	Fetal Kidney	kidney
23	chr6:27357600-27358000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:27357600-27358000	Enhancers	Brain Hippocampus Middle	brain
25	chr6:27357600-27358000	Enhancers	Hela-S3	cervix
26	chr6:27357600-27358200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:27357600-27358200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:27357600-27358200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:27357600-27358400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr6:27357600-27360200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr6:27357600-27362000	Weak transcription	Fetal Stomach	stomach
32	chr6:27357600-27362000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:27357600-27362800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:27357600-27365000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:27357600-27365000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:27357600-27365800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:27357600-27367000	Weak transcription	Fetal Brain Male	brain
38	chr6:27357600-27368000	Weak transcription	Brain Angular Gyrus	brain
39	chr6:27357600-27368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:27357600-27368800	Weak transcription	Pancreas	Pancrea
41	chr6:27357800-27358000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:27357800-27358000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:27357800-27358000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:27357800-27358000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:27357800-27358000	Enhancers	Colon Smooth Muscle	Colon
46	chr6:27357800-27358000	Enhancers	Small Intestine	intestine
47	chr6:27357800-27358000	Enhancers	K562	blood
48	chr6:27357800-27358000	Enhancers	NHEK	skin
49	chr6:27357800-27359400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:27357800-27361000	Weak transcription	Adipose Nuclei	Adipose

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