Variant report

Variant	rs10410424
Chromosome Location	chr19:45603239-45603240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr19:45602464-45603912	MCF-7	breast:	n/a	n/a
2	NR2F2	chr19:45603208-45603879	MCF-7	breast:	n/a	n/a
3	GATA3	chr19:45602559-45603254	SK-N-SH	brain:	n/a	n/a
4	NR2F2	chr19:45602603-45603960	MCF-7	breast:	n/a	n/a
5	MAX	chr19:45603125-45603908	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45572753..45574851-chr19:45600312..45603270,3	MCF-7	breast:
2	chr19:45577259..45585589-chr19:45592358..45603656,27	K562	blood:
3	chr19:45576493..45586900-chr19:45588536..45604492,49	MCF-7	breast:
4	chr19:45578126..45585691-chr19:45599620..45604032,8	MCF-7	breast:

No data

Variant related genes	Relation type
PPP1R37	TF binding region
ENSG00000170684	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000104859	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10402479	0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs10403214	0.93[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405306	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405719	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405721	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406911	1.00[ASN][1000 genomes]
rs10407374	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408462	1.00[ASN][1000 genomes]
rs10409138	0.92[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409232	0.91[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409727	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409903	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412988	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415674	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10417101	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417347	1.00[ASN][1000 genomes]
rs10417618	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417804	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419874	1.00[ASN][1000 genomes]
rs10419883	0.80[YRI][hapmap]
rs10420717	1.00[ASN][1000 genomes]
rs10420824	1.00[ASN][1000 genomes]
rs10421085	1.00[ASN][1000 genomes]
rs10421425	1.00[ASN][1000 genomes]
rs10421932	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs10422671	1.00[ASN][1000 genomes]
rs10423079	1.00[ASN][1000 genomes]
rs10423555	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10424651	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425380	1.00[ASN][1000 genomes]
rs1076384	1.00[ASN][1000 genomes]
rs12459386	1.00[ASN][1000 genomes]
rs12459402	1.00[ASN][1000 genomes]
rs12459945	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461416	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12461749	1.00[ASN][1000 genomes]
rs13344055	0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs13344075	1.00[ASN][1000 genomes]
rs13345307	1.00[ASN][1000 genomes]
rs1541926	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979688	0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs17562676	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17562787	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642665	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982077	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003183	1.00[ASN][1000 genomes]
rs2003345	1.00[ASN][1000 genomes]
rs2004356	1.00[ASN][1000 genomes]
rs2011438	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041261	1.00[ASN][1000 genomes]
rs2041263	1.00[ASN][1000 genomes]
rs2043320	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2060252	1.00[ASN][1000 genomes]
rs2060253	0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs28404390	1.00[ASN][1000 genomes]
rs28657408	1.00[ASN][1000 genomes]
rs28706378	1.00[ASN][1000 genomes]
rs28719739	1.00[ASN][1000 genomes]
rs35904300	1.00[ASN][1000 genomes]
rs4427916	1.00[ASN][1000 genomes]
rs4608431	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803798	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58260098	1.00[ASN][1000 genomes]
rs58600209	1.00[ASN][1000 genomes]
rs58854055	1.00[ASN][1000 genomes]
rs58880456	1.00[ASN][1000 genomes]
rs59240271	1.00[ASN][1000 genomes]
rs60372869	1.00[ASN][1000 genomes]
rs60455813	1.00[ASN][1000 genomes]
rs61531804	1.00[ASN][1000 genomes]
rs7251651	1.00[ASN][1000 genomes]
rs7254138	1.00[ASN][1000 genomes]
rs7257566	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7257599	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259404	1.00[ASN][1000 genomes]
rs733289	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562250	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562267	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73562286	1.00[ASN][1000 genomes]
rs73939607	1.00[ASN][1000 genomes]
rs747646	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs747647	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs754364	0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs754365	1.00[ASN][1000 genomes]
rs754367	0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs8101046	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892133	1.00[ASN][1000 genomes]
rs9653111	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10410424	EIF5AP3	cis	lung	GTEx
rs10410424	Hs.466924	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45604600	Enhancers	Placenta	Placenta
2	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
3	chr19:45597600-45606200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
5	chr19:45597800-45604000	Genic enhancers	Fetal Muscle Leg	muscle
6	chr19:45597800-45604200	Enhancers	Psoas Muscle	Psoas
7	chr19:45598000-45604000	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr19:45598200-45604400	Enhancers	Gastric	stomach
9	chr19:45598200-45606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:45598400-45604000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:45598400-45605600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:45598400-45606000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr19:45598400-45606000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:45598400-45606000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:45598400-45606600	Genic enhancers	Fetal Intestine Small	intestine
16	chr19:45599000-45603600	Genic enhancers	Fetal Thymus	thymus
17	chr19:45599200-45603600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:45599200-45603600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:45599400-45605800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:45599800-45605800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:45600000-45603800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr19:45600000-45604000	Enhancers	HMEC	breast
23	chr19:45600000-45604400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr19:45600000-45606200	Enhancers	Fetal Intestine Large	intestine
25	chr19:45600000-45607800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:45600200-45603600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr19:45600200-45605400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr19:45600400-45604000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:45600400-45604400	Genic enhancers	Fetal Stomach	stomach
30	chr19:45600400-45605000	Weak transcription	GM12878-XiMat	blood
31	chr19:45600600-45603400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr19:45600600-45603600	Enhancers	Fetal Heart	heart
33	chr19:45600800-45603400	Enhancers	Fetal Muscle Trunk	muscle
34	chr19:45600800-45607800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:45601000-45603600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr19:45601000-45603600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr19:45601000-45603800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr19:45601000-45603800	Enhancers	Right Atrium	heart
39	chr19:45601000-45603800	Enhancers	HSMMtube	muscle
40	chr19:45601000-45604600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:45601000-45604600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:45601200-45603600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr19:45601200-45604000	Enhancers	HUVEC	blood vessel
44	chr19:45601400-45603400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr19:45601400-45603600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:45601400-45604400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:45601400-45606200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:45601400-45608000	Enhancers	Esophagus	oesophagus
49	chr19:45601400-45608000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr19:45601600-45603600	Weak transcription	Fetal Brain Female	brain

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