Variant report

Variant	rs10412116
Chromosome Location	chr19:38720538-38720539
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	GTF2F1	chr19:38720442-38720575	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:38720153-38720690	A549	lung:	n/a	n/a
3	SP1	chr19:38720304-38720631	K562	blood:	n/a	chr19:38720534-38720544 chr19:38720535-38720544 chr19:38720533-38720544 chr19:38720533-38720545 chr19:38720499-38720520 chr19:38720533-38720545 chr19:38720534-38720543 chr19:38720534-38720544 chr19:38720559-38720570 chr19:38720535-38720544 chr19:38720530-38720544
4	RCOR1	chr19:38720332-38720793	K562	blood:	n/a	n/a
5	ZEB1	chr19:38720393-38720647	GM12878	blood:	n/a	n/a
6	HDAC2	chr19:38720318-38720702	K562	blood:	n/a	n/a
7	SIN3AK20	chr19:38720109-38720702	PANC-1	pancreas:	n/a	n/a
8	SP4	chr19:38720365-38720672	H1-hESC	embryonic stem cell:	n/a	chr19:38720531-38720547 chr19:38720533-38720544 chr19:38720559-38720570
9	CTCF	chr19:38720292-38720543	K562	blood:	n/a	chr19:38720402-38720415 chr19:38720482-38720492
10	YY1	chr19:38720248-38720575	K562	blood:	n/a	chr19:38720346-38720357
11	CBX3	chr19:38720339-38720680	K562	blood:	n/a	n/a
12	SIX5	chr19:38720289-38720652	K562	blood:	n/a	n/a
13	CTCF	chr19:38720420-38720570	HA-sp	spinal cord:	n/a	chr19:38720482-38720492
14	NFYA	chr19:38720345-38720636	Hela-S3	cervix:	n/a	chr19:38720506-38720521 chr19:38720509-38720519 chr19:38720507-38720521 chr19:38720506-38720521 chr19:38720502-38720520
15	RCOR1	chr19:38720140-38721150	IMR90	lung:	n/a	n/a
16	SIX5	chr19:38720201-38721029	A549	lung:	n/a	n/a
17	EGR1	chr19:38720283-38720556	K562	blood:	n/a	chr19:38720472-38720496 chr19:38720409-38720433
18	RFX5	chr19:38720394-38720583	K562	blood:	n/a	chr19:38720509-38720518
19	JUND	chr19:38720208-38720728	A549	lung:	n/a	chr19:38720508-38720517
20	EGR1	chr19:38720296-38720601	K562	blood:	n/a	chr19:38720472-38720496 chr19:38720409-38720433
21	EBF1	chr19:38720427-38720590	GM12878	blood:	n/a	chr19:38720480-38720491
22	UBTF	chr19:38720176-38720801	K562	blood:	n/a	n/a
23	POLR2A	chr19:38718559-38720966	H1-neurons	neurons:	n/a	n/a
24	HA-E2F1	chr19:38720265-38720886	MCF-7	breast:	n/a	chr19:38720619-38720628 chr19:38720400-38720409
25	YY1	chr19:38720170-38720703	HepG2	liver:	n/a	chr19:38720346-38720357 chr19:38720172-38720181
26	ETS1	chr19:38720377-38720770	A549	lung:	n/a	chr19:38720471-38720484 chr19:38720531-38720544 chr19:38720472-38720485
27	YY1	chr19:38720251-38720730	SK-N-SH_RA	brain:	n/a	chr19:38720346-38720357
28	REST	chr19:38718508-38721161	H1-neurons	neurons:	n/a	chr19:38718827-38718837 chr19:38719471-38719484 chr19:38718636-38718649 chr19:38720543-38720556
29	CTCF	chr19:38720420-38720570	HCPEpiC	choroid plexus:	n/a	chr19:38720482-38720492
30	MYC	chr19:38720368-38720625	K562	blood:	n/a	n/a
31	YY1	chr19:38720251-38720754	H1-hESC	embryonic stem cell:	n/a	chr19:38720346-38720357
32	CTCF	chr19:38720400-38720550	AG10803	skin:	n/a	chr19:38720402-38720415 chr19:38720482-38720492
33	POLR2A	chr19:38718631-38720930	H1-neurons	neurons:	n/a	n/a
34	TCF12	chr19:38720258-38720796	ECC-1	luminal epithelium:	n/a	n/a
35	MXI1	chr19:38720049-38720756	IMR90	lung:	n/a	n/a
36	SP1	chr19:38720310-38720742	HepG2	liver:	n/a	chr19:38720534-38720544 chr19:38720535-38720544 chr19:38720533-38720544 chr19:38720533-38720545 chr19:38720499-38720520 chr19:38720533-38720545 chr19:38720534-38720543 chr19:38720534-38720544 chr19:38720559-38720570 chr19:38720535-38720544 chr19:38720530-38720544
37	NFYB	chr19:38720281-38720697	GM12878	blood:	n/a	chr19:38720506-38720521 chr19:38720509-38720519 chr19:38720507-38720521 chr19:38720506-38720521 chr19:38720508-38720523
38	ELF1	chr19:38720328-38720654	K562	blood:	n/a	n/a
39	SIN3AK20	chr19:38720165-38720835	HCT-116	colon:	n/a	n/a
40	SIX5	chr19:38720275-38720666	GM12878	blood:	n/a	n/a
41	CTCF	chr19:38720500-38720650	A549	lung:	n/a	n/a
42	RCOR1	chr19:38720350-38720769	GM12878	blood:	n/a	n/a
43	HDAC2	chr19:38720251-38720803	MCF-7	breast:	n/a	n/a
44	ETS1	chr19:38720204-38720589	K562	blood:	n/a	chr19:38720471-38720484 chr19:38720531-38720544 chr19:38720472-38720485
45	YY1	chr19:38720269-38720544	GM12892	blood:	n/a	chr19:38720346-38720357
46	YY1	chr19:38720276-38720630	HCT-116	colon:	n/a	chr19:38720346-38720357
47	SIN3A	chr19:38718309-38720711	H1-hESC	embryonic stem cell:	n/a	chr19:38718770-38718781
48	MAZ	chr19:38720241-38720718	K562	blood:	n/a	n/a
49	CTCF	chr19:38720420-38720570	HUVEC	blood vessel:	n/a	chr19:38720482-38720492
50	HCFC1	chr19:38720233-38720723	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38718052..38720655-chr19:38755234..38758069,2	MCF-7	breast:
2	chr19:38711348..38714655-chr19:38718716..38721513,3	MCF-7	breast:
3	chr19:38720504..38722100-chr19:38877148..38880133,2	K562	blood:
4	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
5	chr19:38705043..38707659-chr19:38719005..38721797,2	K562	blood:
6	chr19:38718989..38720789-chr19:38865301..38866855,2	MCF-7	breast:
7	chr19:38720388..38721001-chr19:38825841..38826415,2	K562	blood:
8	chr19:38719348..38721458-chr19:38874867..38876458,2	K562	blood:

Variant related genes	Relation type
DPF1	TF binding region
ENSG00000188766	Chromatin interaction
ENSG00000267090	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000011332	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10401829	1.00[AMR][1000 genomes]
rs10401835	1.00[AMR][1000 genomes]
rs10402883	1.00[AMR][1000 genomes]
rs10403809	1.00[AMR][1000 genomes]
rs10405381	1.00[AMR][1000 genomes]
rs10406765	1.00[AMR][1000 genomes]
rs10407169	1.00[AMR][1000 genomes]
rs10407230	1.00[AMR][1000 genomes]
rs10408479	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408909	1.00[AMR][1000 genomes]
rs10413138	1.00[AMR][1000 genomes]
rs10413363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10413551	1.00[AMR][1000 genomes]
rs10413596	1.00[AMR][1000 genomes]
rs10414916	1.00[AMR][1000 genomes]
rs10414927	1.00[AMR][1000 genomes]
rs10415809	1.00[AMR][1000 genomes]
rs10421241	1.00[AMR][1000 genomes]
rs10423429	1.00[AMR][1000 genomes]
rs10424104	1.00[AMR][1000 genomes]
rs10424818	1.00[AMR][1000 genomes]
rs10425099	1.00[AMR][1000 genomes]
rs10425571	1.00[AMR][1000 genomes]
rs10426292	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28376501	1.00[AMR][1000 genomes]
rs28380555	1.00[AMR][1000 genomes]
rs28421402	1.00[AMR][1000 genomes]
rs28627637	1.00[AMR][1000 genomes]
rs28637743	1.00[AMR][1000 genomes]
rs28649033	1.00[AMR][1000 genomes]
rs28660098	1.00[AMR][1000 genomes]
rs28700884	1.00[AMR][1000 genomes]
rs56134404	1.00[AMR][1000 genomes]
rs56216562	1.00[AMR][1000 genomes]
rs58260561	1.00[AMR][1000 genomes]
rs59571293	1.00[AMR][1000 genomes]
rs61456950	1.00[AMR][1000 genomes]
rs71354969	1.00[AMR][1000 genomes]
rs73630898	1.00[AMR][1000 genomes]
rs73632925	1.00[AMR][1000 genomes]
rs73930357	1.00[AMR][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3419802	chr19:38718712-38720860	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv3405182	chr19:38719137-38721685	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38716600-38720800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr19:38718000-38720800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:38718400-38720600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr19:38718400-38721000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:38718600-38720600	Active TSS	Brain Angular Gyrus	brain
6	chr19:38718600-38720600	Active TSS	Right Ventricle	heart
7	chr19:38718600-38720800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:38718800-38720600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:38718800-38720600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:38718800-38720800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr19:38718800-38720800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:38718800-38720800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:38718800-38721000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:38718800-38721000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr19:38718800-38721200	Active TSS	Brain Germinal Matrix	brain
16	chr19:38718800-38721200	Active TSS	Fetal Brain Female	brain
17	chr19:38719000-38720600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:38719000-38720600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:38719000-38720600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:38719000-38720600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:38719000-38720600	Active TSS	Right Atrium	heart
22	chr19:38719200-38720600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:38719200-38720600	Active TSS	HSMM	muscle
24	chr19:38719200-38720800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:38719200-38720800	Active TSS	Fetal Brain Male	brain
26	chr19:38719200-38721000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr19:38719200-38721000	Active TSS	Brain Cingulate Gyrus	brain
28	chr19:38719400-38720800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:38719400-38721000	Active TSS	Brain Anterior Caudate	brain
30	chr19:38719600-38720600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
31	chr19:38719800-38720600	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr19:38719800-38720600	Active TSS	Hela-S3	cervix
33	chr19:38719800-38720800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:38719800-38720800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
35	chr19:38720000-38720600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:38720000-38720600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr19:38720000-38720600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:38720000-38720600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
39	chr19:38720000-38720600	Bivalent/Poised TSS	A549	lung
40	chr19:38720000-38720600	Weak transcription	NHDF-Ad	bronchial
41	chr19:38720000-38720800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:38720000-38720800	Active TSS	Brain Hippocampus Middle	brain
43	chr19:38720000-38721000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:38720000-38724600	Weak transcription	Fetal Heart	heart
45	chr19:38720200-38720600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:38720200-38720600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:38720200-38720600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:38720200-38720600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr19:38720200-38720800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
50	chr19:38720200-38720800	Bivalent Enhancer	Fetal Muscle Leg	muscle

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