Variant report

Variant	rs10409903
Chromosome Location	chr19:45600991-45600992
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	HNF4A	chr19:45600827-45601256	HepG2	liver:	n/a	chr19:45601044-45601056 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601042-45601057
2	HEY1	chr19:45600865-45601842	HepG2	liver:	n/a	chr19:45601456-45601465
3	SP1	chr19:45600807-45601298	HepG2	liver:	n/a	n/a
4	HNF4G	chr19:45600809-45601197	HepG2	liver:	n/a	chr19:45601034-45601049 chr19:45601044-45601056 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058
5	MAX	chr19:45600825-45602450	HepG2	liver:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
6	ZNF263	chr19:45599899-45602386	HEK293-T-REx	kidney:	n/a	chr19:45601397-45601406
7	MXI1	chr19:45600869-45602519	IMR90	lung:	n/a	chr19:45601457-45601466 chr19:45601455-45601464
8	HNF4A	chr19:45600879-45601260	HepG2	liver:	n/a	chr19:45601044-45601056 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601042-45601057
9	HNF4A	chr19:45600875-45601226	HepG2	liver:	n/a	chr19:45601044-45601056 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601043-45601058 chr19:45601042-45601057
10	ZBTB7A	chr19:45600893-45601115	HepG2	liver:	n/a	n/a
11	MYC	chr19:45600932-45601022	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:45600941-45601139	K562	blood:	n/a	n/a
13	MYC	chr19:45600928-45602055	A549	lung:	n/a	chr19:45601455-45601466 chr19:45601456-45601466 chr19:45601456-45601465 chr19:45601457-45601464
14	HDAC2	chr19:45600870-45601224	HepG2	liver:	n/a	n/a
15	ZBTB7A	chr19:45600649-45601090	HepG2	liver:	n/a	chr19:45600795-45600804

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	chr19:45599536..45601842-chr19:45680214..45683466,3	K562	blood:
5	chr19:45576493..45586900-chr19:45588536..45604492,49	MCF-7	breast:
6	chr19:45600305..45602430-chr19:45642699..45644377,2	K562	blood:
7	chr19:45578126..45585691-chr19:45599620..45604032,8	MCF-7	breast:
8	chr19:45600751..45603096-chr19:45634036..45635702,2	K562	blood:

Variant related genes	Relation type
PPP1R37	TF binding region
ENSG00000170684	Chromatin interaction
ENSG00000104859	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000267545	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406911	1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[ASN][1000 genomes]
rs10407374	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408366	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408462	1.00[CHD][hapmap];0.90[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409727	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];0.93[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];0.88[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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[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];0.84[LWK][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417804	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]
rs10419883	0.81[AFR][1000 genomes]
rs10420717	0.81[AFR][1000 genomes];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	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10423555	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10424651	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425380	0.90[LWK][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1076384	1.00[CHD][hapmap];0.93[LWK][hapmap];0.81[AFR][1000 genomes];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	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13344075	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13345307	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1541926	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979688	0.81[AFR][1000 genomes];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];0.84[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642665	0.95[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	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2003345	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2004356	0.84[AFR][1000 genomes];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];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2060252	1.00[ASN][1000 genomes]
rs2060253	1.00[ASN][1000 genomes]
rs28404390	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28657408	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28706378	0.81[AFR][1000 genomes];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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56764148	0.81[AFR][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];0.97[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];1.00[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];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs747647	1.00[YRI][hapmap];0.84[AFR][1000 genomes];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
rs10409903	EIF5AP3	cis	lung	GTEx
rs10409903	NANOS2	cis	cerebellum	SCAN
rs10409903	DKKL1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45597400-45601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:45597400-45601200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:45597400-45601600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:45597400-45602200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:45597400-45602800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr19:45597400-45603000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr19:45597400-45603000	Enhancers	Fetal Brain Male	brain
8	chr19:45597400-45603200	Enhancers	Left Ventricle	heart
9	chr19:45597400-45604600	Enhancers	Placenta	Placenta
10	chr19:45597400-45609400	Enhancers	Stomach Mucosa	stomach
11	chr19:45597600-45601000	Enhancers	Brain Angular Gyrus	brain
12	chr19:45597600-45601200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr19:45597600-45602000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr19:45597600-45603000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr19:45597600-45603000	Enhancers	Lung	lung
16	chr19:45597600-45606200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:45597600-45609200	Enhancers	Pancreas	Pancrea
18	chr19:45597800-45601000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr19:45597800-45601200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:45597800-45602000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:45597800-45602600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:45597800-45602800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:45597800-45603000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr19:45597800-45604000	Genic enhancers	Fetal Muscle Leg	muscle
25	chr19:45597800-45604200	Enhancers	Psoas Muscle	Psoas
26	chr19:45598000-45601200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr19:45598000-45604000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr19:45598200-45601000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:45598200-45601000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr19:45598200-45601000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:45598200-45601200	Enhancers	Brain Cingulate Gyrus	brain
32	chr19:45598200-45601400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:45598200-45601400	Weak transcription	Fetal Kidney	kidney
34	chr19:45598200-45601800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:45598200-45604400	Enhancers	Gastric	stomach
36	chr19:45598200-45606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr19:45598400-45601000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:45598400-45601000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:45598400-45601000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:45598400-45601000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:45598400-45601000	Enhancers	Duodenum Mucosa	Duodenum
42	chr19:45598400-45601000	Weak transcription	HSMMtube	muscle
43	chr19:45598400-45601200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:45598400-45601200	Enhancers	Brain Hippocampus Middle	brain
45	chr19:45598400-45601200	Weak transcription	HUVEC	blood vessel
46	chr19:45598400-45601200	Genic enhancers	NHLF	lung
47	chr19:45598400-45601400	Enhancers	Adipose Nuclei	Adipose
48	chr19:45598400-45601400	Enhancers	NHDF-Ad	bronchial
49	chr19:45598400-45601600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:45598400-45602200	Enhancers	Colon Smooth Muscle	Colon

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