Variant report

Variant	rs10417804
Chromosome Location	chr19:45595765-45595766
allele	A/C
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	chr19:45595695-45596584	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr19:45595761-45596756	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:45595534-45596827	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:45593947-45597083	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF1	chr19:45595677-45596965	H1-hESC	embryonic stem cell:	n/a	n/a
6	GTF3C2	chr19:45594964-45596224	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:45595714-45597014	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr19:45595724-45596760	K562	blood:	n/a	n/a
9	POLR2A	chr19:45595763-45596656	MCF10A-Er-Src	breast:	n/a	n/a
10	ETS1	chr19:45595702-45596824	K562	blood:	n/a	chr19:45596569-45596580 chr19:45596481-45596492
11	POLR2A	chr19:45595681-45596773	U87	brain:	n/a	n/a
12	REST	chr19:45595721-45596913	A549	lung:	n/a	n/a
13	FOSL2	chr19:45595648-45596618	A549	lung:	n/a	n/a
14	SP1	chr19:45595718-45596636	HCT-116	colon:	n/a	chr19:45596187-45596197 chr19:45596187-45596196 chr19:45596186-45596198 chr19:45596187-45596197 chr19:45596188-45596197 chr19:45596186-45596198 chr19:45596187-45596196 chr19:45596186-45596197
15	POLR2A	chr19:45594165-45596786	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:45595729-45596702	PBDE	blood:	n/a	n/a
17	EP300	chr19:45595761-45596693	ECC-1	luminal epithelium:	n/a	chr19:45596573-45596582
18	POLR2A	chr19:45595760-45596677	K562	blood:	n/a	n/a
19	POLR2A	chr19:45595674-45596304	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:45595598-45596647	U87	brain:	n/a	n/a
21	POLR2A	chr19:45595704-45596654	GM12891	blood:	n/a	n/a
22	TAF1	chr19:45595700-45596670	ECC-1	luminal epithelium:	n/a	n/a
23	SP1	chr19:45595732-45596938	HCT-116	colon:	n/a	chr19:45596187-45596197 chr19:45596805-45596817 chr19:45596187-45596196 chr19:45596806-45596815 chr19:45596186-45596198 chr19:45596807-45596816 chr19:45596805-45596817 chr19:45596187-45596197 chr19:45596188-45596197 chr19:45596186-45596198 chr19:45596187-45596196 chr19:45596186-45596197
24	POLR2A	chr19:45594297-45597124	GM12892	blood:	n/a	n/a
25	EP300	chr19:45595714-45596639	A549	lung:	n/a	chr19:45596573-45596582
26	EP300	chr19:45595674-45596644	A549	lung:	n/a	chr19:45596573-45596582
27	POLR2A	chr19:45594258-45596769	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:45595675-45596773	U87	brain:	n/a	n/a
29	GTF3C2	chr19:45595526-45596249	K562	blood:	n/a	n/a
30	RPC155	chr19:45595655-45596240	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr19:45595677-45596628	K562	blood:	n/a	n/a
32	POLR2A	chr19:45595685-45596720	GM12892	blood:	n/a	n/a
33	POLR2A	chr19:45595676-45596684	HL-60	blood:	n/a	n/a
34	MTA3	chr19:45594524-45596665	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:45595765-45596732	HUVEC	blood vessel:	n/a	n/a
36	PML	chr19:45595653-45597116	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:45595665-45596783	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr19:45595674-45596516	GM12892	blood:	n/a	n/a
39	POLR2A	chr19:45595719-45596947	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr19:45595674-45595870	H1-hESC	embryonic stem cell:	n/a	n/a
41	TEAD4	chr19:45595701-45596515	K562	blood:	n/a	n/a
42	POLR2A	chr19:45594659-45596941	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr19:45594129-45597011	GM12878	blood:	n/a	n/a
44	BCL3	chr19:45595735-45596572	A549	lung:	n/a	chr19:45596476-45596489 chr19:45596051-45596060 chr19:45596484-45596493 chr19:45596481-45596490
45	SIX5	chr19:45595711-45596696	A549	lung:	n/a	n/a
46	SP1	chr19:45595639-45596643	A549	lung:	n/a	chr19:45596187-45596197 chr19:45596187-45596196 chr19:45596186-45596198 chr19:45596187-45596197 chr19:45596188-45596197 chr19:45596186-45596198 chr19:45596187-45596196 chr19:45596186-45596197
47	POLR2A	chr19:45595726-45596603	MCF-7	breast:	n/a	n/a
48	POLR2A	chr19:45595732-45595877	A549	lung:	n/a	n/a
49	POLR2A	chr19:45595681-45595903	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:45595521-45596957	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45571923..45576077-chr19:45594481..45600071,10	MCF-7	breast:
2	chr19:45542175..45544773-chr19:45593754..45596386,2	MCF-7	breast:
3	chr19:45394111..45396115-chr19:45593226..45596136,2	MCF-7	breast:
4	chr19:45594755..45598539-chr19:45681810..45685400,4	K562	blood:
5	chr19:45594874..45597676-chr19:45681810..45683655,2	K562	blood:
6	chr19:45250268..45252334-chr19:45593239..45597540,3	MCF-7	breast:
7	chr19:45577259..45585589-chr19:45592358..45603656,27	K562	blood:
8	chr19:45595033..45597870-chr19:45646652..45650476,4	MCF-7	breast:
9	chr19:45576493..45586900-chr19:45588536..45604492,49	MCF-7	breast:
10	chr19:45576986..45585099-chr19:45592126..45598719,16	MCF-7	breast:
11	chr19:45580763..45587822-chr19:45593153..45598212,14	K562	blood:
12	chr19:45503629..45506931-chr19:45593767..45597738,4	K562	blood:
13	chr19:45542295..45544069-chr19:45594724..45597616,3	MCF-7	breast:
14	chr19:45594586..45596499-chr19:45682181..45685187,4	MCF-7	breast:
15	chr19:45594892..45596535-chr19:45681783..45683354,2	MCF-7	breast:
16	chr19:45594891..45596500-chr19:45754008..45755786,2	MCF-7	breast:
17	chr19:45570935..45574142-chr19:45593620..45597765,5	MCF-7	breast:
18	chr19:45503630..45506563-chr19:45593514..45596516,3	MCF-7	breast:
19	chr19:45593518..45596472-chr19:45847951..45849641,2	MCF-7	breast:

Variant related genes	Relation type
PPP1R37	TF binding region
ENSG00000267348	TF binding region
ENSG00000267282	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000104892	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000069399	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000170684	Chromatin interaction
ENSG00000104856	Chromatin interaction
ENSG00000104859	Chromatin interaction
ENSG00000130204	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10402479	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10403214	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405306	0.95[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406911	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10407374	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408462	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10409138	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409232	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409727	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409903	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410424	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412988	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415674	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10417101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417347	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10417618	0.95[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	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10421425	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10421932	1.00[ASN][1000 genomes]
rs10422671	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10423079	1.00[ASN][1000 genomes]
rs10423555	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10424651	1.00[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	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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17562787	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642665	1.00[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	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2011438	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041261	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2041263	1.00[ASN][1000 genomes]
rs2043320	0.88[AFR][1000 genomes];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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803798	0.95[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	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	0.95[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	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs747647	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs754364	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs754365	1.00[ASN][1000 genomes]
rs754367	0.81[AFR][1000 genomes];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:5 , 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
5	nsv828563	chr19:45594591-45598168	Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10417804	EIF5AP3	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45594000-45598200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:45594200-45597200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:45594200-45597200	Active TSS	Fetal Kidney	kidney
4	chr19:45594200-45597400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:45594200-45597800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:45594200-45598200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr19:45594400-45596200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr19:45594400-45597000	Active TSS	Brain Angular Gyrus	brain
9	chr19:45594400-45597000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:45594400-45597000	Active TSS	Hela-S3	cervix
11	chr19:45594400-45597200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr19:45594400-45597200	Active TSS	Ovary	ovary
13	chr19:45594400-45597400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:45594400-45598200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:45594400-45599200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:45594600-45595800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr19:45594600-45596800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:45594600-45596800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr19:45594600-45597000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:45594600-45597000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:45594600-45597000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:45594600-45597000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr19:45594600-45597000	Active TSS	Brain Germinal Matrix	brain
24	chr19:45594600-45597000	Active TSS	Colon Smooth Muscle	Colon
25	chr19:45594600-45597000	Active TSS	Duodenum Mucosa	Duodenum
26	chr19:45594600-45597000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr19:45594600-45597000	Active TSS	Esophagus	oesophagus
28	chr19:45594600-45597000	Active TSS	Fetal Brain Male	brain
29	chr19:45594600-45597000	Active TSS	Fetal Brain Female	brain
30	chr19:45594600-45597000	Active TSS	Fetal Heart	heart
31	chr19:45594600-45597000	Active TSS	Fetal Lung	lung
32	chr19:45594600-45597000	Active TSS	Fetal Stomach	stomach
33	chr19:45594600-45597000	Active TSS	Lung	lung
34	chr19:45594600-45597000	Active TSS	Pancreas	Pancrea
35	chr19:45594600-45597000	Active TSS	Placenta Amnion	Placenta Amnion
36	chr19:45594600-45597000	Active TSS	Psoas Muscle	Psoas
37	chr19:45594600-45597000	Active TSS	Rectal Smooth Muscle	rectum
38	chr19:45594600-45597000	Active TSS	Stomach Mucosa	stomach
39	chr19:45594600-45597200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:45594600-45597200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:45594600-45597200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:45594600-45597200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:45594600-45597200	Active TSS	Aorta	Aorta
44	chr19:45594600-45597400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:45594600-45597600	Active TSS	A549	lung
46	chr19:45594600-45597600	Active TSS	NHDF-Ad	bronchial
47	chr19:45594800-45596200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:45594800-45596200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:45594800-45596400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr19:45594800-45596400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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