Variant report

Variant	rs10021434
Chromosome Location	chr4:76903295-76903296
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:76903269-76903305	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:76903244-76903427	MCF10A-Er-Src	breast:	n/a	n/a

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

Variant related genes	Relation type
SDAD1	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10007919	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10009947	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029157	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10031733	0.85[CEU][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10031983	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10518143	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12374321	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12374370	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649185	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13112512	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118503	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13129896	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17001247	0.84[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1857821	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242470	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271528	0.83[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276886	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28375800	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28422144	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28451731	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28532601	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28535831	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28588114	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28595360	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28647886	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2869462	0.95[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	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733238	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]
rs3796484	0.89[CEU][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4241577	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4429750	0.84[EUR][1000 genomes]
rs4859567	0.84[CEU][hapmap]
rs4859570	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859571	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859572	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859573	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859577	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859578	0.81[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859580	0.80[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55876513	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66498356	0.89[ASN][1000 genomes]
rs6847815	0.84[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73825589	0.82[AFR][1000 genomes]
rs884004	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884304	0.81[EUR][1000 genomes]
rs9994667	0.83[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10021434	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs10021434	NAAA	cis	Esophagus Muscularis	GTEx
rs10021434	ASAHL	cis	multi-tissue	Pritchard
rs10021434	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs10021434	NAAA	cis	Lymphoblastoid	GTEx
rs10021434	NAAA	cis	Esophagus Mucosa	GTEx
rs10021434	NAAA	cis	Artery Aorta	GTEx
rs10021434	NAAA	cis	Whole Blood	GTEx
rs10021434	NAAA	cis	Muscle Skeletal	GTEx

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	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
3	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
9	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr4:76884600-76903400	Strong transcription	HMEC	breast
11	chr4:76884600-76903400	Strong transcription	HSMM	muscle
12	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:76884800-76903600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:76884800-76903600	Strong transcription	NHEK	skin
17	chr4:76885200-76903800	Strong transcription	Fetal Intestine Large	intestine
18	chr4:76885400-76903600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:76887000-76903800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:76887200-76903400	Strong transcription	Dnd41	blood
21	chr4:76887200-76903600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:76887200-76903800	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr4:76887200-76903800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:76887200-76906000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:76887200-76911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:76887600-76903600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:76887800-76909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:76889800-76903400	Strong transcription	Liver	Liver
29	chr4:76894200-76910200	Weak transcription	Small Intestine	intestine
30	chr4:76894400-76903600	Strong transcription	GM12878-XiMat	blood
31	chr4:76895400-76910400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:76895800-76910200	Weak transcription	Spleen	Spleen
33	chr4:76897600-76910000	Weak transcription	Stomach Mucosa	stomach
34	chr4:76898400-76903400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr4:76898400-76903800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:76898600-76904000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:76898600-76909200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:76899200-76903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:76899200-76903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:76899200-76910200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr4:76899200-76910400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:76899400-76903600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:76899400-76903800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:76899400-76903800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:76899400-76910400	Weak transcription	Fetal Lung	lung
46	chr4:76899800-76903800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr4:76899800-76906600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:76899800-76910000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:76900000-76907000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:76900000-76907200	Weak transcription	Psoas Muscle	Psoas

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