Variant report

Variant	rs3810359
Chromosome Location	chr19:38147031-38147032
allele	A/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	MYC	chr19:38146769-38147173	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:38145479-38147391	HepG2	liver:	n/a	n/a
3	IRF1	chr19:38146767-38147174	K562	blood:	n/a	n/a
4	USF1	chr19:38146834-38147098	SK-N-SH_RA	brain:	n/a	chr19:38146999-38147015
5	TAF1	chr19:38146163-38147341	H1-neurons	neurons:	n/a	n/a
6	WRNIP1	chr19:38146791-38147411	GM12878	blood:	n/a	n/a
7	FOXA1	chr19:38146713-38147195	HepG2	liver:	n/a	n/a
8	STAT5A	chr19:38146548-38147205	GM12878	blood:	n/a	chr19:38146691-38146703
9	MYC	chr19:38146915-38147061	K562	blood:	n/a	n/a
10	ZMIZ1	chr19:38146017-38147202	K562	blood:	n/a	n/a
11	MYC	chr19:38146899-38147109	MCF-7	breast:	n/a	n/a
12	TAF1	chr19:38145897-38147193	ECC-1	luminal epithelium:	n/a	n/a
13	TCF3	chr19:38146601-38147180	GM12878	blood:	n/a	n/a
14	CHD2	chr19:38145886-38147414	K562	blood:	n/a	chr19:38146694-38146704
15	JUND	chr19:38146600-38147259	A549	lung:	n/a	chr19:38147142-38147153 chr19:38146692-38146701
16	USF1	chr19:38146818-38147169	K562	blood:	n/a	chr19:38146999-38147015
17	MAX	chr19:38145396-38147330	MCF-7	breast:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
18	CTCF	chr19:38146980-38147130	GM12873	blood:	n/a	chr19:38147034-38147047
19	EGR1	chr19:38146877-38147169	K562	blood:	n/a	chr19:38147006-38147019 chr19:38147006-38147019 chr19:38147074-38147083
20	POLR2A	chr19:38146093-38147229	HepG2	liver:	n/a	n/a
21	UBTF	chr19:38145350-38147258	K562	blood:	n/a	n/a
22	MAX	chr19:38145158-38147468	A549	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
23	POLR2A	chr19:38145570-38147379	HL-60	blood:	n/a	n/a
24	CBX3	chr19:38146836-38147259	K562	blood:	n/a	n/a
25	E2F6	chr19:38145832-38147266	K562	blood:	n/a	chr19:38147005-38147014 chr19:38146696-38146705 chr19:38146752-38146761
26	ELF1	chr19:38146827-38147199	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:38145969-38147172	A549	lung:	n/a	n/a
28	POLR2A	chr19:38146653-38147218	GM12878	blood:	n/a	n/a
29	GATA2	chr19:38145898-38147392	SH-SY5Y	brain:	n/a	n/a
30	TAF1	chr19:38145639-38147300	HepG2	liver:	n/a	n/a
31	CTCF	chr19:38146980-38147130	HEK293	kidney:	n/a	chr19:38147034-38147047
32	POLR2A	chr19:38146636-38147187	A549	lung:	n/a	n/a
33	POU2F2	chr19:38146665-38147287	GM12878	blood:	n/a	chr19:38146696-38146708
34	BHLHE40	chr19:38146164-38147269	HepG2	liver:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
35	RAD21	chr19:38146864-38147269	HepG2	liver:	n/a	chr19:38147033-38147046 chr19:38147128-38147141
36	POLR2A	chr19:38146727-38147221	H1-hESC	embryonic stem cell:	n/a	n/a
37	CHD2	chr19:38146063-38147264	HepG2	liver:	n/a	chr19:38146694-38146704
38	CEBPB	chr19:38146031-38147033	Hela-S3	cervix:	n/a	n/a
39	REST	chr19:38146104-38147547	H1-neurons	neurons:	n/a	chr19:38146308-38146321 chr19:38146695-38146708
40	CTCF	chr19:38147000-38147150	SK-N-SH_RA	brain:	n/a	chr19:38147034-38147047
41	POLR2A	chr19:38146656-38147250	GM12891	blood:	n/a	n/a
42	ZKSCAN1	chr19:38145626-38147205	Hela-S3	cervix:	n/a	chr19:38146327-38146340
43	BHLHE40	chr19:38145729-38147344	K562	blood:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
44	CTCF	chr19:38146980-38147130	WERI-Rb-1	eye:	n/a	chr19:38147034-38147047
45	CTCF	chr19:38146920-38147070	GM12864	blood:	n/a	chr19:38147034-38147047
46	NRF1	chr19:38145869-38147564	SK-N-SH	brain:	n/a	chr19:38146748-38146762 chr19:38146696-38146705 chr19:38146751-38146765 chr19:38146402-38146411 chr19:38146751-38146760 chr19:38146750-38146761 chr19:38146758-38146767 chr19:38146751-38146762 chr19:38147005-38147014
47	FOXA1	chr19:38146694-38147234	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:38145510-38147461	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:38145590-38147291	MCF-7	breast:	n/a	n/a
50	TBP	chr19:38146081-38147264	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38085961..38087829-chr19:38145172..38147580,2	K562	blood:
2	chr19:37957663..37960695-chr19:38143642..38147199,3	MCF-7	breast:
3	chr19:37958940..37961916-chr19:38146231..38147953,2	K562	blood:

Variant related genes	Relation type
ZFP30	TF binding region
ENSG00000171827	Chromatin interaction
ENSG00000196437	Chromatin interaction
ENSG00000171817	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10153500	0.85[ASN][1000 genomes]
rs10424047	0.80[ASN][1000 genomes]
rs11879149	1.00[ASN][1000 genomes]
rs11880604	1.00[ASN][1000 genomes]
rs34743484	0.90[ASN][1000 genomes]
rs56281742	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57504517	0.80[ASN][1000 genomes]
rs60686304	1.00[ASN][1000 genomes]
rs62108260	0.85[ASN][1000 genomes]
rs62108262	1.00[ASN][1000 genomes]
rs62108264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108289	1.00[ASN][1000 genomes]
rs62108290	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62108292	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62108293	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62108297	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62108302	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62108350	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110193	0.81[EUR][1000 genomes]
rs7245981	0.82[ASN][1000 genomes]
rs7247175	0.95[ASN][1000 genomes]
rs73932929	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8102189	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8104747	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8108261	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38144000-38148000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:38144200-38147200	Active TSS	GM12878-XiMat	blood
3	chr19:38144400-38147600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38144600-38147200	Active TSS	Fetal Kidney	kidney
5	chr19:38144600-38147400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:38144600-38147400	Active TSS	NHDF-Ad	bronchial
7	chr19:38144600-38147600	Active TSS	Fetal Stomach	stomach
8	chr19:38144600-38147600	Active TSS	Hela-S3	cervix
9	chr19:38144600-38147600	Active TSS	NHLF	lung
10	chr19:38144800-38147200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr19:38144800-38147200	Active TSS	Fetal Thymus	thymus
12	chr19:38144800-38147400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:38144800-38147400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:38144800-38147400	Active TSS	Left Ventricle	heart
15	chr19:38144800-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:38144800-38147600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:38144800-38147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:38144800-38147600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:38144800-38147600	Active TSS	Fetal Muscle Trunk	muscle
20	chr19:38145000-38147200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:38145000-38147200	Active TSS	Muscle Satellite Cultured Cells	--
22	chr19:38145000-38147200	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr19:38145000-38147200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:38145000-38147200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:38145000-38147400	Active TSS	Ovary	ovary
26	chr19:38145000-38147400	Active TSS	Right Atrium	heart
27	chr19:38145000-38147600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr19:38145000-38147600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr19:38145000-38147600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:38145000-38147600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:38145000-38147600	Active TSS	Fetal Intestine Large	intestine
32	chr19:38145000-38147600	Active TSS	Psoas Muscle	Psoas
33	chr19:38145000-38147600	Active TSS	HSMM	muscle
34	chr19:38145000-38147600	Active TSS	HSMMtube	muscle
35	chr19:38145000-38147800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:38145200-38147200	Active TSS	Colon Smooth Muscle	Colon
37	chr19:38145200-38147200	Active TSS	Fetal Lung	lung
38	chr19:38145200-38147200	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr19:38145200-38147200	Active TSS	Thymus	Thymus
40	chr19:38145200-38147200	Active TSS	Dnd41	blood
41	chr19:38145200-38147200	Active TSS	NHEK	skin
42	chr19:38145200-38147400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:38145200-38147400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:38145200-38147400	Active TSS	Aorta	Aorta
45	chr19:38145200-38147400	Active TSS	Brain Anterior Caudate	brain
46	chr19:38145200-38147400	Active TSS	Fetal Brain Female	brain
47	chr19:38145200-38147400	Active TSS	Fetal Intestine Small	intestine
48	chr19:38145200-38147400	Active TSS	Placenta Amnion	Placenta Amnion
49	chr19:38145200-38147600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr19:38145200-38147800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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