Variant report

Variant	rs73035160
Chromosome Location	chr19:38146036-38146037
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	chr19:38145722-38146625	A549	lung:	n/a	n/a
2	POLR2A	chr19:38145479-38147391	HepG2	liver:	n/a	n/a
3	ZMIZ1	chr19:38146017-38147202	K562	blood:	n/a	n/a
4	TAF1	chr19:38145897-38147193	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr19:38145610-38146611	A549	lung:	n/a	chr19:38146299-38146315 chr19:38146429-38146445
6	JUND	chr19:38145818-38146582	A549	lung:	n/a	chr19:38146408-38146417 chr19:38146241-38146255
7	RUNX3	chr19:38145587-38146280	GM12878	blood:	n/a	n/a
8	YY1	chr19:38145590-38146658	GM12878	blood:	n/a	n/a
9	CHD2	chr19:38145886-38147414	K562	blood:	n/a	chr19:38146694-38146704
10	MAX	chr19:38145396-38147330	MCF-7	breast:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
11	PAX5	chr19:38145491-38146076	GM12878	blood:	n/a	chr19:38145747-38145766 chr19:38145749-38145767
12	UBTF	chr19:38145350-38147258	K562	blood:	n/a	n/a
13	MAX	chr19:38145158-38147468	A549	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
14	POLR2A	chr19:38145570-38147379	HL-60	blood:	n/a	n/a
15	E2F6	chr19:38145832-38147266	K562	blood:	n/a	chr19:38147005-38147014 chr19:38146696-38146705 chr19:38146752-38146761
16	POLR2A	chr19:38145969-38147172	A549	lung:	n/a	n/a
17	POLR2A	chr19:38145482-38146938	Hela-S3	cervix:	n/a	n/a
18	GATA2	chr19:38145898-38147392	SH-SY5Y	brain:	n/a	n/a
19	TAF1	chr19:38145639-38147300	HepG2	liver:	n/a	n/a
20	UBTF	chr19:38145491-38147030	K562	blood:	n/a	n/a
21	THAP1	chr19:38146026-38146177	K562	blood:	n/a	n/a
22	SPI1	chr19:38145932-38146086	K562	blood:	n/a	n/a
23	CEBPB	chr19:38146031-38147033	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr19:38146006-38146856	K562	blood:	n/a	n/a
25	ZKSCAN1	chr19:38145626-38147205	Hela-S3	cervix:	n/a	chr19:38146327-38146340
26	BHLHE40	chr19:38145729-38147344	K562	blood:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
27	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
28	POLR2A	chr19:38145510-38147461	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr19:38145590-38147291	MCF-7	breast:	n/a	n/a
30	SPI1	chr19:38145712-38146094	GM12878	blood:	n/a	n/a
31	MAZ	chr19:38145365-38147377	IMR90	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
32	MAX	chr19:38145131-38147074	Hela-S3	cervix:	n/a	chr19:38146453-38146462 chr19:38146550-38146559
33	POLR2A	chr19:38145503-38147263	GM12891	blood:	n/a	n/a
34	YY1	chr19:38145964-38147139	GM12878	blood:	n/a	chr19:38146696-38146705 chr19:38146683-38146697
35	POLR2A	chr19:38145503-38147000	Raji	blood:	n/a	n/a
36	POLR2A	chr19:38145590-38147197	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:38145572-38147031	Hela-S3	cervix:	n/a	n/a
38	REST	chr19:38145712-38146514	SK-N-SH	brain:	n/a	chr19:38146308-38146321 chr19:38145908-38145917
39	GTF2F1	chr19:38144883-38146955	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr19:38145469-38147313	HepG2	liver:	n/a	n/a
41	SIN3A	chr19:38145970-38147104	GM12878	blood:	n/a	n/a
42	SIN3A	chr19:38145518-38147279	H1-hESC	embryonic stem cell:	n/a	n/a
43	HMGN3	chr19:38145989-38147266	K562	blood:	n/a	n/a
44	CTCF	chr19:38145980-38146130	RPTEC	kidney:	n/a	n/a
45	POLR2A	chr19:38145423-38147229	GM19099	blood:	n/a	n/a
46	POLR2A	chr19:38146010-38146142	A549	lung:	n/a	n/a
47	HEY1	chr19:38146033-38147380	HepG2	liver:	n/a	chr19:38146690-38146705 chr19:38146440-38146455
48	CHD2	chr19:38145732-38147464	GM12878	blood:	n/a	chr19:38146694-38146704
49	E2F6	chr19:38146006-38147283	A549	lung:	n/a	chr19:38147005-38147014 chr19:38146696-38146705 chr19:38146752-38146761
50	MAZ	chr19:38145614-38147240	K562	blood:	n/a	chr19:38146453-38146462 chr19:38146550-38146559

No.	Distal block	Cell Line	Cell type
1	chr15:75932176..75933046-chr19:38146017..38146882,2	Hela-S3	cervix:
2	chr19:38145174..38146985-chr19:38184008..38186251,2	MCF-7	breast:
3	chr19:38085961..38087829-chr19:38145172..38147580,2	K562	blood:
4	chr19:37957663..37960695-chr19:38143642..38147199,3	MCF-7	breast:
5	chr19:37960304..37962188-chr19:38144303..38146867,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF781-2	chr19:38145948-38146366	NONHSAT066151

Variant related genes	Relation type
ZFP30	TF binding region
ENSG00000171827	Chromatin interaction
ENSG00000171817	Chromatin interaction
ENSG00000267319	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000196437	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10445548	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.86[ASN][1000 genomes]
rs1871196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.99[EUR][1000 genomes]
rs57943942	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62108291	0.84[EUR][1000 genomes]
rs62108306	0.83[EUR][1000 genomes]
rs7245855	0.86[ASN][1000 genomes]
rs7259272	0.83[EUR][1000 genomes]
rs73031330	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs73035160	AC012309.5	cis	Esophagus Mucosa	GTEx
rs73035160	AC012309.5	cis	Thyroid	GTEx
rs73035160	AC012309.5	cis	Muscle Skeletal	GTEx
rs73035160	AC012309.5	cis	Heart Left Ventricle	GTEx
rs73035160	ZNF781	cis	Thyroid	GTEx
rs73035160	AC012309.5	cis	Esophagus Muscularis	GTEx
rs73035160	AC012309.5	cis	Artery Tibial	GTEx
rs73035160	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx

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	chr19:38144400-38146200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:38144400-38147600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:38144600-38146800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:38144600-38147000	Active TSS	A549	lung
7	chr19:38144600-38147200	Active TSS	Fetal Kidney	kidney
8	chr19:38144600-38147400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:38144600-38147400	Active TSS	NHDF-Ad	bronchial
10	chr19:38144600-38147600	Active TSS	Fetal Stomach	stomach
11	chr19:38144600-38147600	Active TSS	Hela-S3	cervix
12	chr19:38144600-38147600	Active TSS	NHLF	lung
13	chr19:38144800-38146200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr19:38144800-38146200	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr19:38144800-38146600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:38144800-38147200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr19:38144800-38147200	Active TSS	Fetal Thymus	thymus
18	chr19:38144800-38147400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:38144800-38147400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:38144800-38147400	Active TSS	Left Ventricle	heart
21	chr19:38144800-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr19:38144800-38147600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr19:38144800-38147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:38144800-38147600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:38144800-38147600	Active TSS	Fetal Muscle Trunk	muscle
26	chr19:38145000-38146200	Active TSS	Fetal Brain Male	brain
27	chr19:38145000-38147000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:38145000-38147000	Active TSS	Right Ventricle	heart
29	chr19:38145000-38147000	Active TSS	Stomach Smooth Muscle	stomach
30	chr19:38145000-38147200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:38145000-38147200	Active TSS	Muscle Satellite Cultured Cells	--
32	chr19:38145000-38147200	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr19:38145000-38147200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:38145000-38147200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:38145000-38147400	Active TSS	Ovary	ovary
36	chr19:38145000-38147400	Active TSS	Right Atrium	heart
37	chr19:38145000-38147600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr19:38145000-38147600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr19:38145000-38147600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:38145000-38147600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:38145000-38147600	Active TSS	Fetal Intestine Large	intestine
42	chr19:38145000-38147600	Active TSS	Psoas Muscle	Psoas
43	chr19:38145000-38147600	Active TSS	HSMM	muscle
44	chr19:38145000-38147600	Active TSS	HSMMtube	muscle
45	chr19:38145000-38147800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:38145200-38146200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr19:38145200-38147000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:38145200-38147000	Active TSS	Placenta	Placenta
49	chr19:38145200-38147200	Active TSS	Colon Smooth Muscle	Colon
50	chr19:38145200-38147200	Active TSS	Fetal Lung	lung

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