Variant report

Variant	rs10413896
Chromosome Location	chr19:42585833-42585834
allele	G/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	RAD21	chr19:42585808-42585963	K562	blood:	n/a	chr19:42585911-42585918 chr19:42585835-42585844
2	ELF1	chr19:42585701-42586289	A549	lung:	n/a	n/a
3	CTCF	chr19:42585726-42586097	IMR90	lung:	n/a	n/a
4	CTCF	chr19:42585814-42586006	GM10266	blood:	n/a	n/a
5	CTCF	chr19:42585820-42585970	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr19:42585648-42586136	A549	lung:	n/a	chr19:42585911-42585918 chr19:42585835-42585844
7	TBL1XR1	chr19:42585826-42586048	GM12878	blood:	n/a	n/a
8	RAD21	chr19:42585766-42586157	MCF-7	breast:	n/a	chr19:42585911-42585918 chr19:42585835-42585844
9	MYC	chr19:42585825-42585924	MCF-7	breast:	n/a	n/a
10	POLR2A	chr19:42585596-42586465	SK-N-MC	brain:	n/a	n/a
11	CTCF	chr19:42585796-42586004	GM10248	blood:	n/a	n/a
12	POLR2A	chr19:42585760-42586569	U87	brain:	n/a	n/a
13	CTCF	chr19:42585820-42585970	HFF-Myc	foreskin:	n/a	n/a
14	POLR2A	chr19:42585485-42586475	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:42583992-42586924	K562	blood:	n/a	n/a
16	POLR2A	chr19:42585787-42586121	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr19:42585785-42586033	HepG2	liver:	n/a	n/a
18	CTCF	chr19:42585814-42586012	Kidney_OC	kidney:	n/a	n/a
19	CTCF	chr19:42585826-42585996	GM13976	blood:	n/a	n/a
20	CTCF	chr19:42585770-42586049	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:42585624-42586152	K562	blood:	n/a	n/a
22	RAD21	chr19:42585739-42586113	IMR90	lung:	n/a	chr19:42585911-42585918 chr19:42585835-42585844
23	CTCF	chr19:42585820-42585970	NHEK	skin:	n/a	n/a
24	CTCF	chr19:42585766-42585963	SK-N-SH_RA	brain:	n/a	n/a
25	POLR2A	chr19:42585570-42586099	HL-60	blood:	n/a	n/a
26	CTCF	chr19:42585811-42586034	Medullo	brain:	n/a	n/a
27	POLR2A	chr19:42585734-42586479	HepG2	liver:	n/a	n/a
28	CTCF	chr19:42585802-42586027	GM13977	blood:	n/a	n/a
29	RCOR1	chr19:42585817-42586037	K562	blood:	n/a	n/a
30	CTCF	chr19:42585820-42585970	GM12872	blood:	n/a	n/a
31	CTCF	chr19:42585800-42585950	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:42585277-42586107	GM12891	blood:	n/a	n/a
33	POLR2A	chr19:42583521-42586597	GM12878	blood:	n/a	n/a
34	CTCF	chr19:42585800-42585950	HRPEpiC	eye:	n/a	n/a
35	POLR2A	chr19:42585537-42586373	K562	blood:	n/a	n/a
36	POLR2A	chr19:42585752-42585945	GM12878	blood:	n/a	n/a
37	RAD21	chr19:42585753-42586070	SK-N-SH_RA	brain:	n/a	chr19:42585911-42585918 chr19:42585835-42585844
38	POLR2A	chr19:42584852-42586106	H1-neurons	neurons:	n/a	n/a
39	CTCF	chr19:42585820-42585970	GM12875	blood:	n/a	n/a
40	CTCF	chr19:42585816-42585988	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr19:42585785-42586033	Spleen_OC	spleen:	n/a	n/a
42	RAD21	chr19:42585763-42586110	HepG2	liver:	n/a	chr19:42585911-42585918 chr19:42585835-42585844
43	MYC	chr19:42585704-42585976	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr19:42585213-42586506	A549	lung:	n/a	n/a
45	CTCF	chr19:42585820-42585970	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:42585762-42586318	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr19:42585820-42585970	AG04450	lung:	n/a	n/a
48	CTCF	chr19:42585762-42586067	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr19:42585767-42586030	A549	lung:	n/a	n/a
50	CTCF	chr19:42585820-42585970	GM12867	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42585326..42588805-chr19:42593865..42598286,4	MCF-7	breast:
2	chr19:42554804..42557504-chr19:42584494..42586137,2	MCF-7	breast:
3	chr19:42585189..42586779-chr19:42682804..42685130,2	K562	blood:

Variant related genes	Relation type
ENSG00000268525	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10414151	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13347017	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73552850	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv911783	chr19:42575462-42624662	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42582000-42587800	Weak transcription	Fetal Kidney	kidney
2	chr19:42582000-42590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:42582200-42586600	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr19:42582200-42587200	Strong transcription	Fetal Muscle Leg	muscle
5	chr19:42582200-42588400	Strong transcription	Lung	lung
6	chr19:42582200-42596000	Weak transcription	Right Atrium	heart
7	chr19:42582200-42597800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:42582400-42586000	Strong transcription	Liver	Liver
9	chr19:42582400-42586200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:42582400-42586200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:42582400-42586400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:42582400-42586400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:42582400-42586400	Strong transcription	Primary T cells from cord blood	blood
14	chr19:42582400-42586600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:42582400-42586600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:42582400-42586600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:42582400-42586600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:42582400-42586600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr19:42582400-42586600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:42582400-42586600	Strong transcription	Brain Angular Gyrus	brain
21	chr19:42582400-42586600	Strong transcription	Brain Hippocampus Middle	brain
22	chr19:42582400-42586600	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr19:42582400-42586600	Strong transcription	Fetal Thymus	thymus
24	chr19:42582400-42586600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr19:42582400-42588200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:42582400-42588400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:42582400-42588800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:42582400-42588800	Strong transcription	Fetal Stomach	stomach
29	chr19:42582400-42592800	Weak transcription	HSMMtube	muscle
30	chr19:42582400-42594000	Weak transcription	Fetal Brain Male	brain
31	chr19:42582400-42594800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:42582400-42595600	Weak transcription	Fetal Heart	heart
33	chr19:42582400-42595800	Weak transcription	Hela-S3	cervix
34	chr19:42582400-42597800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:42582600-42586000	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr19:42582600-42586000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:42582600-42586000	Strong transcription	Brain Cingulate Gyrus	brain
38	chr19:42582600-42586000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:42582600-42586000	Strong transcription	Gastric	stomach
40	chr19:42582600-42586000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr19:42582600-42586200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:42582600-42586200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr19:42582600-42586200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:42582600-42586200	Strong transcription	Brain Substantia Nigra	brain
45	chr19:42582600-42586400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:42582600-42586400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr19:42582600-42586400	Strong transcription	Primary B cells from cord blood	blood
48	chr19:42582600-42586400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr19:42582600-42586600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:42582600-42586600	Strong transcription	Primary T cells fromperipheralblood	blood

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