Variant report

Variant	rs10419074
Chromosome Location	chr19:56879136-56879137
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	CBX3	chr19:56879131-56879765	K562	blood:	n/a	n/a
2	POLR2A	chr19:56879131-56880092	H1-neurons	neurons:	n/a	n/a
3	NRF1	chr19:56878841-56880268	SK-N-SH	brain:	n/a	chr19:56879429-56879440 chr19:56879430-56879444 chr19:56879430-56879441 chr19:56879427-56879441 chr19:56879430-56879439
4	POLR2A	chr19:56879079-56880006	PFSK-1	brain:	n/a	n/a
5	REST	chr19:56878877-56880429	H1-neurons	neurons:	n/a	chr19:56879371-56879391
6	POLR2A	chr19:56879135-56880116	K562	blood:	n/a	n/a
7	TBL1XR1	chr19:56879046-56879625	K562	blood:	n/a	n/a
8	POLR2A	chr19:56879052-56880080	HUVEC	blood vessel:	n/a	n/a
9	RCOR1	chr19:56879080-56879685	K562	blood:	n/a	n/a
10	MAX	chr19:56879129-56880225	A549	lung:	n/a	n/a
11	MAX	chr19:56879092-56880116	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56878151..56881655-chr19:56903333..56906269,7	K562	blood:
2	chr19:56874655..56877497-chr19:56878126..56879780,2	K562	blood:
3	chr19:56878056..56881655-chr19:56903333..56906269,5	K562	blood:

Variant related genes	Relation type
ENSG00000267606	TF binding region
ZNF542	TF binding region
ENSG00000018869	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000267606	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1017102	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs10401898	0.98[ASN][1000 genomes]
rs10403419	0.93[YRI][hapmap]
rs10405914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10413341	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10414446	0.93[YRI][hapmap]
rs10418348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10419213	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12608516	0.82[CEU][hapmap];0.89[MEX][hapmap]
rs12608563	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12610246	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12981331	0.82[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap]
rs12982404	0.82[CEU][hapmap]
rs12983342	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs12983411	1.00[CEU][hapmap];0.98[ASN][1000 genomes]
rs2288856	0.83[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2304123	0.82[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs2304125	0.82[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs2304126	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304127	0.82[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs4334405	0.88[ASN][1000 genomes]
rs4462708	0.82[CEU][hapmap]
rs4801717	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8111942	0.83[CHB][hapmap];0.92[CHD][hapmap]

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	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56872200-56879400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:56873800-56879200	Weak transcription	Left Ventricle	heart
3	chr19:56877400-56879200	Weak transcription	Ovary	ovary
4	chr19:56878800-56879200	Active TSS	Liver	Liver
5	chr19:56878800-56879200	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr19:56878800-56879600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:56878800-56880200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:56878800-56880200	Active TSS	Brain Cingulate Gyrus	brain
9	chr19:56878800-56880400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr19:56878800-56880600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:56878800-56880600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:56878800-56880600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:56878800-56880800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr19:56879000-56879200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:56879000-56879200	Enhancers	Primary B cells from peripheral blood	blood
16	chr19:56879000-56879200	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:56879000-56879200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr19:56879000-56879200	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr19:56879000-56879200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:56879000-56879200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56879000-56879200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:56879000-56879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:56879000-56879200	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr19:56879000-56879200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr19:56879000-56879200	Flanking Active TSS	Fetal Heart	heart
26	chr19:56879000-56879200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr19:56879000-56879200	ZNF genes & repeats	A549	lung
28	chr19:56879000-56879200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr19:56879000-56879400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr19:56879000-56879400	Flanking Active TSS	K562	blood
31	chr19:56879000-56879600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr19:56879000-56879600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr19:56879000-56879600	Active TSS	Fetal Muscle Trunk	muscle
34	chr19:56879000-56879800	Active TSS	Primary hematopoietic stem cells	blood
35	chr19:56879000-56879800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:56879000-56880000	Active TSS	Primary T cells from cord blood	blood
37	chr19:56879000-56880000	Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr19:56879000-56880000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr19:56879000-56880000	Active TSS	Adipose Nuclei	Adipose
40	chr19:56879000-56880000	Active TSS	Brain Angular Gyrus	brain
41	chr19:56879000-56880000	Active TSS	Stomach Smooth Muscle	stomach
42	chr19:56879000-56880000	Active TSS	NH-A	brain
43	chr19:56879000-56880200	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr19:56879000-56880200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:56879000-56880200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:56879000-56880200	Active TSS	Brain Germinal Matrix	brain
47	chr19:56879000-56880200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr19:56879000-56880200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:56879000-56880200	Active TSS	Brain Substantia Nigra	brain
50	chr19:56879000-56880200	Active TSS	Colon Smooth Muscle	Colon

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