Variant report

Variant	rs6806440
Chromosome Location	chr3:141627538-141627539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141625787..141627994-chr3:141631487..141633848,2	K562	blood:
2	chr3:141621597..141625746-chr3:141627353..141630692,4	MCF-7	breast:
3	chr3:141607282..141610185-chr3:141626378..141628187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200389	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11915071	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11926859	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2068231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115938	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28454329	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28463227	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4511872	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58370035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767100	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773662	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782993	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801868	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6804938	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6805115	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73230628	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7616510	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7624456	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642890	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648330	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9849347	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9853609	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6806440	ATP1B3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
3	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
4	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:141618000-141633600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:141619400-141641600	Weak transcription	Ovary	ovary
9	chr3:141619600-141628400	Weak transcription	Psoas Muscle	Psoas
10	chr3:141619600-141640200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:141619600-141644000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:141619800-141633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:141620400-141641200	Weak transcription	Spleen	Spleen
14	chr3:141620600-141631600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:141620800-141646800	Weak transcription	Gastric	stomach
16	chr3:141621000-141646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
18	chr3:141622000-141645000	Strong transcription	Dnd41	blood
19	chr3:141622000-141647600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:141622200-141628600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:141622200-141628800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:141622200-141628800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:141622200-141630800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:141622200-141631400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:141622200-141631600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:141622400-141629400	Strong transcription	Hela-S3	cervix
27	chr3:141622400-141631600	Strong transcription	Fetal Intestine Small	intestine
28	chr3:141622400-141647000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:141622600-141631800	Strong transcription	NHEK	skin
30	chr3:141622600-141633200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:141622600-141644800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:141622800-141628800	Strong transcription	HepG2	liver
33	chr3:141622800-141629800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:141623000-141627600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:141623200-141628600	Strong transcription	Placenta	Placenta
36	chr3:141623600-141629000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:141623600-141629400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:141623600-141630600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
40	chr3:141623800-141628800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:141623800-141628800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr3:141623800-141629200	Strong transcription	HUVEC	blood vessel
43	chr3:141623800-141629200	Strong transcription	K562	blood
44	chr3:141623800-141629400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:141623800-141629800	Strong transcription	GM12878-XiMat	blood
46	chr3:141623800-141631600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:141624000-141628400	Strong transcription	A549	lung
48	chr3:141624000-141628800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr3:141624000-141629200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:141624000-141629400	Strong transcription	Primary T cells fromperipheralblood	blood

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