Variant report

Variant	rs3733238
Chromosome Location	chr4:76902739-76902740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76902021..76904810-chr4:76904972..76908899,4	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10007919	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10009947	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10021434	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029157	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10031733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10031983	0.82[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10518143	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12374321	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12374370	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649185	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13111494	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs13112512	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118503	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13129896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13130917	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs17001247	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][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];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1857821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242470	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271528	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276886	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28375800	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28422144	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28451731	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28532601	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28535831	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28588114	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28595360	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28647886	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2869462	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34630680	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34740469	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4241577	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4429750	0.84[EUR][1000 genomes]
rs4859567	1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4859570	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859572	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859573	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859577	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859578	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859580	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859609	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs55876513	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66498356	0.89[ASN][1000 genomes]
rs6847815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs884004	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884304	0.81[EUR][1000 genomes]
rs9994667	0.82[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3733238	NAAA	cis	Artery Aorta	GTEx
rs3733238	NAAA	cis	Muscle Skeletal	GTEx
rs3733238	NAAA	cis	parietal	SCAN
rs3733238	FAM47E	cis	cerebellum	SCAN
rs3733238	CDKL2	cis	parietal	SCAN
rs3733238	NAAA	cis	Whole Blood	GTEx
rs3733238	NAAA	cis	lymphoblastoid	seeQTL
rs3733238	NAAA	cis	Esophagus Mucosa	GTEx
rs3733238	NAAA	cis	Esophagus Muscularis	GTEx
rs3733238	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs3733238	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs3733238	CXCL10	cis	lymphoblastoid	seeQTL
rs3733238	NAAA	cis	cerebellum	SCAN
rs3733238	RCHY1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
4	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
12	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:76883800-76903000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:76884000-76902800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:76884200-76902800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr4:76884600-76902800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:76884600-76902800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:76884600-76902800	Strong transcription	Adipose Nuclei	Adipose
20	chr4:76884600-76903400	Strong transcription	HMEC	breast
21	chr4:76884600-76903400	Strong transcription	HSMM	muscle
22	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:76884800-76903600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:76884800-76903600	Strong transcription	NHEK	skin
27	chr4:76885000-76903000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr4:76885200-76903800	Strong transcription	Fetal Intestine Large	intestine
29	chr4:76885400-76903600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:76887000-76903800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:76887200-76903400	Strong transcription	Dnd41	blood
32	chr4:76887200-76903600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:76887200-76903800	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr4:76887200-76903800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:76887200-76906000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:76887200-76911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:76887600-76903600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:76887800-76909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:76889800-76903400	Strong transcription	Liver	Liver
40	chr4:76894200-76910200	Weak transcription	Small Intestine	intestine
41	chr4:76894400-76903600	Strong transcription	GM12878-XiMat	blood
42	chr4:76895000-76903000	Strong transcription	Brain Anterior Caudate	brain
43	chr4:76895400-76910400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:76895800-76910200	Weak transcription	Spleen	Spleen
45	chr4:76896600-76902800	Strong transcription	HSMMtube	muscle
46	chr4:76897600-76910000	Weak transcription	Stomach Mucosa	stomach
47	chr4:76897800-76902800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr4:76897800-76903200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:76898200-76903000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:76898400-76903400	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links