Variant report

Variant	rs10415478
Chromosome Location	chr19:42796169-42796170
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	POLR2A	chr19:42794973-42796169	HepG2	liver:	n/a	n/a
2	CTCF	chr19:42794168-42796267	A549	lung:	n/a	chr19:42795920-42795928
3	POLR2A	chr19:42794908-42801736	H1-neurons	neurons:	n/a	n/a
4	BCL3	chr19:42795776-42796311	A549	lung:	n/a	n/a
5	POLR2A	chr19:42796160-42796398	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:42796051-42796339	K562	blood:	n/a	n/a
7	POLR2A	chr19:42794882-42797816	K562	blood:	n/a	n/a
8	POLR2A	chr19:42794782-42796358	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr19:42794399-42798142	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr19:42796166-42796360	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:42795122-42797717	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:42796106-42796295	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:42794916-42797620	K562	blood:	n/a	n/a
14	POLR2A	chr19:42793952-42801695	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr19:42795255-42796269	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
2	chr19:42595218..42597830-chr19:42795165..42796711,2	K562	blood:
3	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:

Variant related genes	Relation type
CIC	TF binding region
ENSG00000268643	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000105722	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10401224	0.85[YRI][hapmap]
rs10403246	1.00[AMR][1000 genomes]
rs10406755	1.00[AMR][1000 genomes]
rs10408141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409428	0.85[YRI][hapmap]
rs10409433	0.85[YRI][hapmap]
rs10410129	0.85[YRI][hapmap]
rs10410653	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs10412954	1.00[AMR][1000 genomes]
rs10413484	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs10414056	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10414620	0.92[YRI][hapmap]
rs10416241	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10418493	1.00[AMR][1000 genomes]
rs10419013	1.00[AMR][1000 genomes]
rs10421026	1.00[AMR][1000 genomes]
rs10421409	0.85[YRI][hapmap]
rs10425883	1.00[AMR][1000 genomes]
rs11880356	0.85[YRI][hapmap]
rs13343322	0.85[YRI][hapmap]
rs13345986	1.00[AMR][1000 genomes]
rs28469564	0.81[AFR][1000 genomes]
rs28532592	1.00[AMR][1000 genomes]
rs28572784	1.00[YRI][hapmap]
rs28699037	0.81[AFR][1000 genomes]
rs35620536	1.00[AMR][1000 genomes]
rs6509012	1.00[AMR][1000 genomes]
rs7258727	0.85[YRI][hapmap]
rs73552850	1.00[AMR][1000 genomes]
rs8099885	0.85[YRI][hapmap]
rs8109258	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
9	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
10	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42790200-42800200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:42790600-42797800	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr19:42790600-42801600	Strong transcription	Dnd41	blood
4	chr19:42790600-42802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:42790600-42804600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:42790600-42804800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:42790600-42805000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:42790600-42805400	Weak transcription	Stomach Mucosa	stomach
9	chr19:42790600-42806000	Weak transcription	Psoas Muscle	Psoas
10	chr19:42790800-42799000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:42790800-42802000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:42790800-42802200	Strong transcription	Thymus	Thymus
13	chr19:42791000-42799200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:42791000-42799600	Strong transcription	HSMMtube	muscle
15	chr19:42791000-42799800	Strong transcription	Lung	lung
16	chr19:42791000-42800200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:42791000-42800200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:42791000-42801400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:42791000-42801600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr19:42791000-42801600	Strong transcription	NHLF	lung
21	chr19:42791000-42802800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:42791200-42796200	Strong transcription	HUVEC	blood vessel
23	chr19:42791200-42796600	Strong transcription	Primary hematopoietic stem cells	blood
24	chr19:42791200-42798600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:42791200-42799000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:42791200-42799000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:42791200-42799000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:42791200-42799000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:42791200-42799000	Strong transcription	Adipose Nuclei	Adipose
30	chr19:42791200-42799000	Strong transcription	Aorta	Aorta
31	chr19:42791200-42799200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:42791200-42799200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr19:42791200-42799400	Strong transcription	Primary T cells from cord blood	blood
34	chr19:42791200-42799400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:42791200-42799600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:42791200-42799800	Strong transcription	Liver	Liver
37	chr19:42791200-42800000	Strong transcription	Spleen	Spleen
38	chr19:42791200-42800200	Strong transcription	GM12878-XiMat	blood
39	chr19:42791200-42800400	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:42791200-42801400	Strong transcription	Osteobl	bone
41	chr19:42791200-42801600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:42791200-42804600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:42791200-42805800	Weak transcription	Fetal Heart	heart
44	chr19:42791200-42806000	Weak transcription	Right Atrium	heart
45	chr19:42791400-42797600	Strong transcription	Fetal Lung	lung
46	chr19:42791400-42797800	Strong transcription	NH-A	brain
47	chr19:42791400-42798400	Strong transcription	HepG2	liver
48	chr19:42791400-42798800	Strong transcription	Brain Anterior Caudate	brain
49	chr19:42791400-42798800	Strong transcription	Brain Substantia Nigra	brain
50	chr19:42791400-42799000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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