Variant report

Variant	rs10420443
Chromosome Location	chr19:45657258-45657259
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	POLR2A	chr19:45656816-45658087	PFSK-1	brain:	n/a	n/a
2	FOXA1	chr19:45657221-45657774	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr19:45656944-45657306	K562	blood:	n/a	n/a
4	EGR1	chr19:45656988-45657403	K562	blood:	n/a	chr19:45657203-45657212 chr19:45657200-45657213 chr19:45657200-45657213 chr19:45657200-45657214 chr19:45657200-45657213 chr19:45657199-45657214 chr19:45657080-45657090 chr19:45657081-45657091 chr19:45657201-45657212 chr19:45657200-45657213 chr19:45657202-45657212 chr19:45657202-45657212 chr19:45657076-45657089
5	MAX	chr19:45656651-45658096	HepG2	liver:	n/a	chr19:45657081-45657091 chr19:45657936-45657951 chr19:45657940-45657949 chr19:45657936-45657945
6	POLR2A	chr19:45657171-45658145	HepG2	liver:	n/a	n/a
7	UBTF	chr19:45657170-45657370	K562	blood:	n/a	n/a
8	FOXP2	chr19:45656644-45657393	PFSK-1	brain:	n/a	n/a
9	E2F6	chr19:45655175-45657423	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOXA1	chr19:45657157-45658083	HepG2	liver:	n/a	n/a
11	MAX	chr19:45655239-45657363	H1-hESC	embryonic stem cell:	n/a	chr19:45657081-45657091
12	MAZ	chr19:45657029-45658052	K562	blood:	n/a	chr19:45657081-45657091 chr19:45657936-45657951 chr19:45657940-45657949 chr19:45657936-45657945
13	GABPA	chr19:45656565-45657383	H1-hESC	embryonic stem cell:	n/a	chr19:45657081-45657090
14	MYC	chr19:45656794-45657259	K562	blood:	n/a	chr19:45657081-45657091
15	EGR1	chr19:45657008-45658316	HCT-116	colon:	n/a	chr19:45657203-45657212 chr19:45657200-45657213 chr19:45657200-45657213 chr19:45657200-45657214 chr19:45657200-45657213 chr19:45657199-45657214 chr19:45657080-45657090 chr19:45657081-45657091 chr19:45657201-45657212 chr19:45657200-45657213 chr19:45657202-45657212 chr19:45657202-45657212 chr19:45657076-45657089
16	JUN	chr19:45656734-45658282	K562	blood:	n/a	n/a
17	POLR2A	chr19:45656659-45657433	SK-N-MC	brain:	n/a	n/a
18	FOXA1	chr19:45657251-45657759	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:45656740-45657367	H1-neurons	neurons:	n/a	n/a
20	GABPA	chr19:45657020-45657313	K562	blood:	n/a	chr19:45657081-45657090
21	POLR2A	chr19:45656975-45657291	K562	blood:	n/a	n/a
22	POLR2A	chr19:45656836-45657648	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr19:45654849-45658095	IMR90	lung:	n/a	chr19:45657939-45657948 chr19:45657937-45657946
24	KAP1	chr19:45656669-45657984	HEK293	kidney:	n/a	n/a
25	GABPA	chr19:45656463-45657368	H1-hESC	embryonic stem cell:	n/a	chr19:45657081-45657090
26	ELF1	chr19:45657017-45657390	K562	blood:	n/a	chr19:45657233-45657246
27	EGR1	chr19:45656977-45657362	K562	blood:	n/a	chr19:45657203-45657212 chr19:45657200-45657213 chr19:45657200-45657213 chr19:45657200-45657214 chr19:45657200-45657213 chr19:45657199-45657214 chr19:45657080-45657090 chr19:45657081-45657091 chr19:45657201-45657212 chr19:45657200-45657213 chr19:45657202-45657212 chr19:45657202-45657212 chr19:45657076-45657089
28	NR2F2	chr19:45657133-45658306	K562	blood:	n/a	n/a
29	MXI1	chr19:45655414-45657598	SK-N-SH	brain:	n/a	n/a
30	NR3C1	chr19:45657206-45658301	A549	lung:	n/a	chr19:45657768-45657794 chr19:45657774-45657788 chr19:45657772-45657790 chr19:45657768-45657794 chr19:45657770-45657791 chr19:45657829-45657842 chr19:45657768-45657794 chr19:45657781-45657788 chr19:45657768-45657794 chr19:45657768-45657794
31	NR3C1	chr19:45656487-45658216	A549	lung:	n/a	chr19:45657768-45657794 chr19:45657774-45657788 chr19:45657772-45657790 chr19:45657768-45657794 chr19:45657770-45657791 chr19:45657829-45657842 chr19:45657768-45657794 chr19:45657781-45657788 chr19:45657768-45657794 chr19:45657768-45657794
32	ELF1	chr19:45656855-45657362	K562	blood:	n/a	chr19:45657233-45657246
33	FOXA1	chr19:45657224-45657904	HepG2	liver:	n/a	n/a
34	MAX	chr19:45655290-45657356	H1-hESC	embryonic stem cell:	n/a	chr19:45657081-45657091
35	UBTF	chr19:45657117-45657298	K562	blood:	n/a	n/a
36	RCOR1	chr19:45656976-45658202	K562	blood:	n/a	n/a
37	EGR1	chr19:45656927-45657401	H1-hESC	embryonic stem cell:	n/a	chr19:45657203-45657212 chr19:45657200-45657213 chr19:45657200-45657213 chr19:45657200-45657214 chr19:45657200-45657213 chr19:45657199-45657214 chr19:45657080-45657090 chr19:45657081-45657091 chr19:45657201-45657212 chr19:45657200-45657213 chr19:45657202-45657212 chr19:45657202-45657212 chr19:45657076-45657089
38	POLR2A	chr19:45656710-45658058	K562	blood:	n/a	n/a
39	BHLHE40	chr19:45656163-45657367	GM12878	blood:	n/a	n/a
40	MAX	chr19:45656624-45657374	K562	blood:	n/a	chr19:45657081-45657091
41	CREB1	chr19:45656786-45658110	HepG2	liver:	n/a	n/a
42	ELF1	chr19:45657125-45657396	HepG2	liver:	n/a	chr19:45657233-45657246
43	E2F6	chr19:45655264-45657260	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr19:45656672-45658123	HCT-116	colon:	n/a	chr19:45657081-45657091 chr19:45657936-45657951 chr19:45657940-45657949 chr19:45657936-45657945

No.	Distal block	Cell Line	Cell type
1	chr19:45655086..45657605-chr19:45680853..45682730,2	MCF-7	breast:
2	chr19:45651718..45653898-chr19:45656029..45658572,2	K562	blood:
3	chr19:45646614..45649721-chr19:45656300..45659382,4	K562	blood:
4	chr19:45654421..45658397-chr19:45679888..45682724,3	K562	blood:
5	chr19:45640971..45644367-chr19:45655076..45659170,3	K562	blood:

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000267037	TF binding region
ENSG00000267037	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000007255	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12459851	1.00[AMR][1000 genomes]
rs12460007	1.00[AMR][1000 genomes]
rs12460771	1.00[AMR][1000 genomes]
rs4427916	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv3347313	chr19:45654737-45657285	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45651800-45660200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:45654600-45658000	Bivalent Enhancer	Placenta	Placenta
3	chr19:45654800-45657400	Bivalent Enhancer	Fetal Brain Male	brain
4	chr19:45654800-45660400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:45655000-45657400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:45655000-45657400	Enhancers	Fetal Heart	heart
7	chr19:45655000-45657400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
8	chr19:45655000-45657600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:45655200-45657400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr19:45655200-45657400	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr19:45655200-45657400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr19:45655200-45657400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:45655200-45657400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
14	chr19:45655200-45657400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:45655200-45657400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
16	chr19:45655200-45658000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:45655400-45657400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr19:45655400-45657400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:45655400-45657400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
20	chr19:45655400-45657400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
21	chr19:45655600-45657400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:45655600-45657400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
23	chr19:45655600-45657400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:45655600-45657400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:45655600-45657400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr19:45655600-45657400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr19:45655600-45657400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
28	chr19:45655600-45657600	Enhancers	Primary hematopoietic stem cells	blood
29	chr19:45655600-45657600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr19:45655600-45657600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:45655800-45657400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:45655800-45657400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
33	chr19:45656000-45657400	Flanking Active TSS	Ovary	ovary
34	chr19:45656000-45658000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr19:45656200-45657400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:45656200-45657400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
37	chr19:45656200-45657400	Flanking Bivalent TSS/Enh	Thymus	Thymus
38	chr19:45656200-45657800	Enhancers	Gastric	stomach
39	chr19:45656400-45657400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:45656400-45657800	Enhancers	Lung	lung
41	chr19:45656400-45658000	Bivalent Enhancer	Fetal Thymus	thymus
42	chr19:45656400-45658000	Bivalent Enhancer	Spleen	Spleen
43	chr19:45656400-45658000	Bivalent Enhancer	NHDF-Ad	bronchial
44	chr19:45656600-45657400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr19:45656600-45657400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr19:45656600-45657400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:45656600-45657400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
48	chr19:45656600-45657800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:45656600-45658000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:45656800-45657400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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