Variant report

Variant	rs3796544
Chromosome Location	chr4:57215677-57215678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57215250..57218405-chr4:57219428..57221610,3	K562	blood:
2	chr4:57209917..57212599-chr4:57213686..57216147,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1042040	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1124570	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11538098	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11722404	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11723379	0.83[EUR][1000 genomes]
rs11728068	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11732985	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11734595	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935357	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11937997	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11943048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11946745	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13102012	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs13109030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13114481	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13122196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122422	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13123542	0.86[ASN][1000 genomes]
rs13124065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13124696	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs13129188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13131846	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13132553	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13134963	0.85[CEU][hapmap]
rs13135151	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140746	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146014	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13148435	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13148656	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];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13150137	0.80[ASN][1000 genomes]
rs13150967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401908	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1401911	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030363	0.83[EUR][1000 genomes]
rs2176785	0.85[CEU][hapmap]
rs6554346	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554347	0.89[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs6554350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554353	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554354	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811153	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6811616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6811652	0.83[EUR][1000 genomes]
rs6812222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818283	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6818340	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6820922	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6823339	0.85[EUR][1000 genomes]
rs6854326	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6857561	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7437329	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7654543	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7656361	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673373	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7682041	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682608	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7695701	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs956275	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9995463	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3796544	RPL21P44	cis	cerebellum	SCAN
rs3796544	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs3796544	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs3796544	AASDH	cis	parietal	SCAN
rs3796544	AASDH	cis	multi-tissue	Pritchard
rs3796544	AASDH	cis	cerebellum	SCAN
rs3796544	AASDH	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
2	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
3	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
4	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
7	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
8	chr4:57203200-57235200	Weak transcription	Osteobl	bone
9	chr4:57203200-57251800	Weak transcription	A549	lung
10	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:57204000-57216800	Weak transcription	Hela-S3	cervix
13	chr4:57204000-57252200	Weak transcription	NH-A	brain
14	chr4:57204200-57222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:57204200-57227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:57204800-57223400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
20	chr4:57205000-57217200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:57205000-57223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:57205000-57228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:57205200-57228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:57205200-57229200	Weak transcription	Brain Germinal Matrix	brain
25	chr4:57205400-57228000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:57208800-57222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:57210600-57222400	Weak transcription	Thymus	Thymus
29	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:57211200-57216200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:57211800-57216200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:57211800-57217600	Strong transcription	Liver	Liver
33	chr4:57211800-57218400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
35	chr4:57212000-57216200	Strong transcription	Adipose Nuclei	Adipose
36	chr4:57212000-57221000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:57212200-57216200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:57212600-57216400	Strong transcription	Primary T cells from cord blood	blood
40	chr4:57212800-57216000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:57212800-57216200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:57212800-57216600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr4:57212800-57217600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:57213000-57216000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr4:57213000-57216200	Strong transcription	Fetal Brain Female	brain
46	chr4:57213000-57216600	Strong transcription	Left Ventricle	heart
47	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
48	chr4:57213200-57229200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:57213400-57216000	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:57213400-57216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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