Variant report

Variant	rs7740487
Chromosome Location	chr6:28216486-28216487
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28198177..28200363-chr6:28214686..28217029,3	MCF-7	breast:
2	chr6:28116033..28118585-chr6:28214732..28216735,2	MCF-7	breast:
3	chr6:28215636..28217426-chr6:28225443..28228209,2	MCF-7	breast:
4	chr6:28207533..28210874-chr6:28216267..28219988,4	MCF-7	breast:
5	chr6:28202226..28208942-chr6:28209296..28217649,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189134	Chromatin interaction
ENSG00000187626	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10456362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11755032	0.88[ASN][1000 genomes]
rs11965538	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13200462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1339899	0.87[ASN][1000 genomes]
rs1419183	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1679709	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679732	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778507	0.91[ASN][1000 genomes]
rs1778508	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778511	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1936365	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2743554	0.94[ASN][1000 genomes]
rs2743555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799077	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799079	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68141011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905391	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6920512	0.90[ASN][1000 genomes]
rs735765	0.92[EUR][1000 genomes]
rs853676	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853678	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853679	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853681	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853682	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs853685	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853688	0.86[ASN][1000 genomes]
rs853694	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366717	0.81[EUR][1000 genomes]
rs9368561	0.80[EUR][1000 genomes]
rs9393908	0.81[EUR][1000 genomes]
rs9461446	0.91[ASN][1000 genomes]
rs9461448	0.88[ASN][1000 genomes]
rs9461449	0.88[ASN][1000 genomes]
rs9468321	0.91[ASN][1000 genomes]
rs9468322	0.91[ASN][1000 genomes]
rs9986596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7740487	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs7740487	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs7740487	AL022393.7	cis	Muscle Skeletal	GTEx
rs7740487	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs7740487	RP5-874C20.3	cis	Thyroid	GTEx
rs7740487	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs7740487	RP5-874C20.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28193800-28218400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:28193800-28218400	Weak transcription	Stomach Mucosa	stomach
3	chr6:28201600-28219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:28203000-28218400	Weak transcription	HUVEC	blood vessel
5	chr6:28211000-28216800	Strong transcription	Brain Germinal Matrix	brain
6	chr6:28211000-28217200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:28211000-28217200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:28211000-28217600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:28211000-28217600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:28211000-28217600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:28211000-28217600	Strong transcription	Placenta	Placenta
12	chr6:28211200-28216800	Strong transcription	Primary B cells from cord blood	blood
13	chr6:28211200-28217000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:28211200-28217400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:28211200-28217600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:28211400-28217000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:28211600-28216600	Strong transcription	Fetal Stomach	stomach
18	chr6:28211600-28216800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:28211600-28217000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:28211600-28217000	Strong transcription	Liver	Liver
21	chr6:28211600-28217600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:28211600-28217600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr6:28211600-28217600	Strong transcription	Left Ventricle	heart
24	chr6:28211600-28217600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:28211600-28217600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr6:28211600-28217800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:28211600-28218000	Strong transcription	Fetal Muscle Leg	muscle
28	chr6:28211800-28217200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:28211800-28217400	Strong transcription	Primary T cells from cord blood	blood
30	chr6:28211800-28217400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:28211800-28217600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:28211800-28217800	Strong transcription	Fetal Thymus	thymus
33	chr6:28212000-28217000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:28212000-28217600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:28212000-28217600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:28212000-28217600	Strong transcription	Adipose Nuclei	Adipose
37	chr6:28212000-28217800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:28212000-28217800	Strong transcription	Brain Substantia Nigra	brain
39	chr6:28212200-28216600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:28212200-28216600	Strong transcription	Fetal Intestine Large	intestine
41	chr6:28212200-28217000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:28212200-28217400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:28212200-28217800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:28212400-28216600	Strong transcription	Fetal Intestine Small	intestine
45	chr6:28212400-28216800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr6:28212400-28217200	Strong transcription	GM12878-XiMat	blood
47	chr6:28212400-28217600	Strong transcription	Fetal Lung	lung
48	chr6:28212600-28217600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:28212600-28217800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:28212800-28216600	Strong transcription	Primary hematopoietic stem cells	blood

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