Variant report

Variant	rs10409727
Chromosome Location	chr19:45602862-45602863
allele	C/T
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	GATA3	chr19:45602464-45603912	MCF-7	breast:	n/a	n/a
2	JUND	chr19:45602769-45603147	HepG2	liver:	n/a	chr19:45602953-45602964
3	POLR2A	chr19:45602766-45602893	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:45602771-45602889	MCF-7	breast:	n/a	n/a
5	JUND	chr19:45602804-45603058	HepG2	liver:	n/a	chr19:45602953-45602964
6	GATA3	chr19:45602559-45603254	SK-N-SH	brain:	n/a	n/a
7	GATA2	chr19:45602733-45603125	HUVEC	blood vessel:	n/a	n/a
8	FOSL2	chr19:45602652-45603188	HepG2	liver:	n/a	chr19:45602954-45602965
9	MAZ	chr19:45602784-45602916	K562	blood:	n/a	n/a
10	JUN	chr19:45602821-45603011	K562	blood:	n/a	n/a
11	GATA3	chr19:45602720-45603136	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr19:45602821-45603076	MCF-7	breast:	n/a	n/a
13	TCF7L2	chr19:45602756-45603071	MCF-7	breast:	n/a	n/a
14	FOSL2	chr19:45602739-45603102	HepG2	liver:	n/a	chr19:45602954-45602965
15	GATA3	chr19:45602679-45603223	MCF-7	breast:	n/a	n/a
16	BHLHE40	chr19:45602805-45603134	HepG2	liver:	n/a	n/a
17	JUND	chr19:45602757-45603105	HepG2	liver:	n/a	chr19:45602953-45602964
18	BHLHE40	chr19:45602820-45603090	K562	blood:	n/a	n/a
19	JUND	chr19:45602753-45603124	K562	blood:	n/a	chr19:45602953-45602964
20	NR2F2	chr19:45602603-45603960	MCF-7	breast:	n/a	n/a
21	RCOR1	chr19:45602854-45602903	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45572753..45574851-chr19:45600312..45603270,3	MCF-7	breast:
2	chr19:45600364..45603096-chr19:45634036..45635975,3	K562	blood:
3	chr19:45577259..45585589-chr19:45592358..45603656,27	K562	blood:
4	chr19:45576493..45586900-chr19:45588536..45604492,49	MCF-7	breast:
5	chr19:45578126..45585691-chr19:45599620..45604032,8	MCF-7	breast:
6	chr19:45600751..45603096-chr19:45634036..45635702,2	K562	blood:

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

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10402479	0.82[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405719	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405721	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406911	1.00[CHD][hapmap];0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs10407374	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	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]
rs10408462	1.00[CHD][hapmap];0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs10409138	0.92[CEU][hapmap];1.00[CHD][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409232	0.91[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][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]
rs10410424	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]
rs10412988	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415674	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10417101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[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[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MKK][hapmap];0.96[TSI][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]
rs10417804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419874	1.00[ASN][1000 genomes]
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[CHB][hapmap];1.00[ASN][1000 genomes]
rs10422671	1.00[ASN][1000 genomes]
rs10423079	1.00[ASN][1000 genomes]
rs10423555	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10424651	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425380	0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs1076384	1.00[CHD][hapmap];0.87[LWK][hapmap];1.00[ASN][1000 genomes]
rs11881409	1.00[CHD][hapmap]
rs12459074	0.80[CEU][hapmap]
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	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	1.00[ASN][1000 genomes]
rs17562676	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17562787	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642665	0.91[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[CHD][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2060252	1.00[ASN][1000 genomes]
rs2060253	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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803798	0.96[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[CHD][hapmap];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];0.93[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];0.96[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	1.00[ASN][1000 genomes]
rs754365	1.00[ASN][1000 genomes]
rs754367	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10409727	DKKL1	cis	cerebellum	SCAN
rs10409727	NANOS2	cis	cerebellum	SCAN
rs10409727	EIF5AP3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45603000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr19:45597400-45603000	Enhancers	Fetal Brain Male	brain
3	chr19:45597400-45603200	Enhancers	Left Ventricle	heart
4	chr19:45597400-45604600	Enhancers	Placenta	Placenta
5	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
6	chr19:45597600-45603000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr19:45597600-45603000	Enhancers	Lung	lung
8	chr19:45597600-45606200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
10	chr19:45597800-45603000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr19:45597800-45604000	Genic enhancers	Fetal Muscle Leg	muscle
12	chr19:45597800-45604200	Enhancers	Psoas Muscle	Psoas
13	chr19:45598000-45604000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr19:45598200-45604400	Enhancers	Gastric	stomach
15	chr19:45598200-45606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr19:45598400-45604000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:45598400-45605600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:45598400-45606000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr19:45598400-45606000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:45598400-45606000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:45598400-45606600	Genic enhancers	Fetal Intestine Small	intestine
22	chr19:45599000-45603600	Genic enhancers	Fetal Thymus	thymus
23	chr19:45599200-45603600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:45599200-45603600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:45599400-45605800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr19:45599800-45603000	Genic enhancers	Spleen	Spleen
27	chr19:45599800-45605800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:45600000-45603800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr19:45600000-45604000	Enhancers	HMEC	breast
30	chr19:45600000-45604400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr19:45600000-45606200	Enhancers	Fetal Intestine Large	intestine
32	chr19:45600000-45607800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:45600200-45603000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr19:45600200-45603600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:45600200-45605400	Enhancers	Placenta Amnion	Placenta Amnion
36	chr19:45600400-45604000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:45600400-45604400	Genic enhancers	Fetal Stomach	stomach
38	chr19:45600400-45605000	Weak transcription	GM12878-XiMat	blood
39	chr19:45600600-45603000	Flanking Active TSS	HepG2	liver
40	chr19:45600600-45603400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr19:45600600-45603600	Enhancers	Fetal Heart	heart
42	chr19:45600800-45603400	Enhancers	Fetal Muscle Trunk	muscle
43	chr19:45600800-45607800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:45601000-45603600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr19:45601000-45603600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr19:45601000-45603800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr19:45601000-45603800	Enhancers	Right Atrium	heart
48	chr19:45601000-45603800	Enhancers	HSMMtube	muscle
49	chr19:45601000-45604600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:45601000-45604600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links