Variant report

Variant	rs10403517
Chromosome Location	chr19:42973862-42973863
allele	A/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	FOS	chr19:42973754-42973889	MCF10A-Er-Src	breast:	n/a	n/a
2	JUN	chr19:42973760-42973950	HepG2	liver:	n/a	n/a
3	CEBPB	chr19:42973655-42974238	A549	lung:	n/a	chr19:42973787-42973798
4	CEBPB	chr19:42973633-42974302	HepG2	liver:	n/a	chr19:42973787-42973798
5	JUND	chr19:42973646-42973930	HepG2	liver:	n/a	chr19:42973777-42973788
6	CEBPB	chr19:42973644-42973867	IMR90	lung:	n/a	chr19:42973787-42973798
7	FOSL2	chr19:42973672-42973942	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNU4-60P	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10084159	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10401271	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10402361	0.84[AMR][1000 genomes]
rs10402677	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10404402	0.81[AFR][1000 genomes]
rs10405445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405646	0.87[AMR][1000 genomes]
rs10405906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10407576	0.88[CEU][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes]
rs10411458	0.81[AFR][1000 genomes]
rs10412463	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10413413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415564	0.80[AMR][1000 genomes]
rs10416089	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10417418	0.80[AMR][1000 genomes]
rs10417693	0.80[AMR][1000 genomes]
rs10419378	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10420796	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10421108	0.86[AMR][1000 genomes]
rs10422987	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10423291	0.81[AFR][1000 genomes]
rs10469271	0.87[AMR][1000 genomes]
rs10469284	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10469286	0.88[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs1076243	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11083659	0.86[AMR][1000 genomes]
rs11665870	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11665935	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666835	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11666862	0.87[AMR][1000 genomes]
rs11668599	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671272	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671846	0.85[EUR][1000 genomes]
rs11673645	0.85[EUR][1000 genomes]
rs11879306	0.88[EUR][1000 genomes]
rs11881517	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11882150	0.88[EUR][1000 genomes]
rs12611218	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13343936	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16975789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16975865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975890	0.83[EUR][1000 genomes]
rs1859341	0.80[AMR][1000 genomes]
rs2267631	0.88[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs28411988	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28447294	0.80[AMR][1000 genomes]
rs4080606	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4499340	0.80[AMR][1000 genomes]
rs55850134	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60313903	0.85[EUR][1000 genomes]
rs6509016	0.87[AFR][1000 genomes]
rs7248297	0.86[AMR][1000 genomes]
rs7253056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253209	0.86[AMR][1000 genomes]
rs8102439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102519	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8103285	0.88[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8103891	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8106083	0.80[AMR][1000 genomes]
rs8106570	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8107152	0.88[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8107254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107790	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8108844	0.86[YRI][hapmap]
rs8112156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851298	0.85[EUR][1000 genomes]
rs851301	0.88[EUR][1000 genomes]
rs851302	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9304604	0.93[YRI][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr19:42969400-42975200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr19:42970000-42974600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr19:42970600-42976400	Enhancers	HSMM	muscle
6	chr19:42970800-42974600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:42970800-42974800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:42970800-42975000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:42970800-42975600	Weak transcription	Stomach Mucosa	stomach
10	chr19:42971000-42975400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:42971000-42975800	Weak transcription	Colonic Mucosa	Colon
12	chr19:42971000-42978000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:42971200-42974000	Weak transcription	Placenta	Placenta
14	chr19:42971200-42975600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:42971600-42975000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:42971600-42978000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:42971600-42979000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:42971800-42975600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:42972200-42974200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:42972400-42974400	Enhancers	Fetal Muscle Leg	muscle
21	chr19:42972600-42974000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:42972600-42975200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:42972600-42975400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:42972600-42979200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr19:42972800-42974000	Weak transcription	HMEC	breast
26	chr19:42972800-42974400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:42972800-42975200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:42972800-42975200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:42972800-42975400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:42972800-42975600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr19:42972800-42975800	Weak transcription	Fetal Intestine Small	intestine
32	chr19:42972800-42976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:42972800-42977000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr19:42973000-42975800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:42973200-42974400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:42973400-42974000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:42973400-42974200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr19:42973400-42974200	Enhancers	HSMMtube	muscle
39	chr19:42973400-42974400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:42973400-42974400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr19:42973400-42974400	Enhancers	Primary B cells from peripheral blood	blood
42	chr19:42973400-42974400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:42973400-42974400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:42973400-42974600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr19:42973400-42976400	Enhancers	HepG2	liver
46	chr19:42973600-42974400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:42973600-42974400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:42973600-42974600	Enhancers	Primary B cells from cord blood	blood
49	chr19:42973800-42974000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:42973800-42974000	Enhancers	Muscle Satellite Cultured Cells	--

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