Variant report

Variant	rs4713139
Chromosome Location	chr6:28092685-28092686
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28092672..28095102-chr6:28302623..28304601,2	MCF-7	breast:
2	chr6:27858930..27860939-chr6:28090408..28092869,2	MCF-7	breast:
3	chr6:28091137..28098786-chr6:28103559..28111884,14	MCF-7	breast:
4	chr6:28069766..28072466-chr6:28092411..28094495,2	MCF-7	breast:
5	chr6:28092149..28093653-chr6:28108097..28109825,2	MCF-7	breast:
6	chr6:28089193..28090739-chr6:28092491..28094959,2	MCF-7	breast:
7	chr6:28092067..28092954-chr6:28104224..28105168,3	MCF-7	breast:
8	chr6:28083288..28085321-chr6:28091167..28093208,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000219392	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10456362	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs11965538	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs12055625	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs13200462	0.93[CEU][hapmap]
rs1321504	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1321505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437126	1.00[ASN][1000 genomes]
rs13437444	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1419183	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs149943	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs149990	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs1679709	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs1679732	0.93[CEU][hapmap]
rs16893573	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs16893601	1.00[CHB][hapmap]
rs16893735	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17720293	0.85[CEU][hapmap]
rs1778507	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs1778508	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs1778511	0.93[CEU][hapmap]
rs202906	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2799077	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs2799079	0.93[CEU][hapmap]
rs34130214	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712084	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3757188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713138	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4713140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs6920512	0.90[YRI][hapmap]
rs735765	0.93[CEU][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180562	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904142	0.90[CHD][hapmap]
rs9295765	1.00[YRI][hapmap]
rs9348792	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9357064	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9366717	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9368560	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9368561	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380030	0.90[CHD][hapmap]
rs9380031	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs9380032	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9380051	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9380064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380069	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs9393882	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs9393889	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9393902	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9393908	0.80[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9461432	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461439	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9461446	0.81[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9468287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468300	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468301	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9468321	1.00[YRI][hapmap]
rs9468322	0.81[GIH][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4713139	BTN3A2	trans	lymphoblastoid	seeQTL
rs4713139	LRRC16A	cis	parietal	SCAN
rs4713139	RP5-874C20.3	cis	Thyroid	GTEx
rs4713139	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs4713139	VCAN	trans	lymphoblastoid	seeQTL
rs4713139	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs4713139		cis	Lymphoblastoid	GTEx
rs4713139	ZNF323	cis	parietal	SCAN
rs4713139	ZNF192	cis	cerebellum	SCAN
rs4713139	AL022393.7	cis	Muscle Skeletal	GTEx
rs4713139	ZSCAN23	cis	cerebellum	SCAN
rs4713139	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28082600-28096200	Strong transcription	Dnd41	blood
2	chr6:28091200-28096600	Strong transcription	K562	blood
3	chr6:28091600-28093000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:28091600-28093200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:28091600-28093200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:28091600-28093200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:28091600-28093600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:28091800-28092800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr6:28091800-28092800	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr6:28091800-28092800	Active TSS	Fetal Stomach	stomach
11	chr6:28091800-28092800	Active TSS	Stomach Mucosa	stomach
12	chr6:28091800-28092800	Active TSS	HSMM	muscle
13	chr6:28091800-28092800	Active TSS	NHLF	lung
14	chr6:28091800-28093000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:28091800-28093000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:28091800-28093000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:28091800-28093000	Active TSS	Psoas Muscle	Psoas
18	chr6:28091800-28093000	Active TSS	Right Atrium	heart
19	chr6:28091800-28093000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr6:28091800-28093000	Active TSS	Thymus	Thymus
21	chr6:28091800-28093000	Active TSS	GM12878-XiMat	blood
22	chr6:28091800-28093000	Active TSS	HSMMtube	muscle
23	chr6:28091800-28093200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:28091800-28093200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28091800-28093200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:28091800-28093200	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:28091800-28093200	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:28091800-28093200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr6:28091800-28093200	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:28091800-28093200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:28091800-28093200	Active TSS	Stomach Smooth Muscle	stomach
32	chr6:28091800-28093400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr6:28091800-28093400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr6:28091800-28093600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:28092000-28092800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:28092000-28092800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:28092000-28092800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:28092000-28092800	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr6:28092000-28092800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:28092000-28092800	Active TSS	Brain Anterior Caudate	brain
41	chr6:28092000-28092800	Active TSS	Brain Cingulate Gyrus	brain
42	chr6:28092000-28092800	Active TSS	Brain Hippocampus Middle	brain
43	chr6:28092000-28092800	Active TSS	Brain Substantia Nigra	brain
44	chr6:28092000-28092800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:28092000-28092800	Active TSS	Small Intestine	intestine
46	chr6:28092000-28092800	Active TSS	Hela-S3	cervix
47	chr6:28092000-28092800	Active TSS	NHDF-Ad	bronchial
48	chr6:28092000-28093000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:28092000-28093000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr6:28092000-28093000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links