Variant report

Variant	rs1871196
Chromosome Location	chr19:38146923-38146924
allele	A/C
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	PML	chr19:38146702-38147025	GM12878	blood:	n/a	n/a
6	TAF1	chr19:38146163-38147341	H1-neurons	neurons:	n/a	n/a
7	WRNIP1	chr19:38146791-38147411	GM12878	blood:	n/a	n/a
8	FOXA1	chr19:38146713-38147195	HepG2	liver:	n/a	n/a
9	STAT5A	chr19:38146548-38147205	GM12878	blood:	n/a	chr19:38146691-38146703
10	MYC	chr19:38146915-38147061	K562	blood:	n/a	n/a
11	ZMIZ1	chr19:38146017-38147202	K562	blood:	n/a	n/a
12	MYC	chr19:38146899-38147109	MCF-7	breast:	n/a	n/a
13	TAF1	chr19:38145897-38147193	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr19:38146780-38146930	GM12868	blood:	n/a	n/a
15	TCF3	chr19:38146601-38147180	GM12878	blood:	n/a	n/a
16	CHD2	chr19:38145886-38147414	K562	blood:	n/a	chr19:38146694-38146704
17	JUND	chr19:38146600-38147259	A549	lung:	n/a	chr19:38147142-38147153 chr19:38146692-38146701
18	USF1	chr19:38146818-38147169	K562	blood:	n/a	chr19:38146999-38147015
19	MAX	chr19:38145396-38147330	MCF-7	breast:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
20	EGR1	chr19:38146877-38147169	K562	blood:	n/a	chr19:38147006-38147019 chr19:38147006-38147019 chr19:38147074-38147083
21	POLR2A	chr19:38146093-38147229	HepG2	liver:	n/a	n/a
22	UBTF	chr19:38145350-38147258	K562	blood:	n/a	n/a
23	MAX	chr19:38145158-38147468	A549	lung:	n/a	chr19:38146453-38146462 chr19:38147300-38147309 chr19:38146550-38146559
24	POLR2A	chr19:38145570-38147379	HL-60	blood:	n/a	n/a
25	CBX3	chr19:38146836-38147259	K562	blood:	n/a	n/a
26	E2F6	chr19:38145832-38147266	K562	blood:	n/a	chr19:38147005-38147014 chr19:38146696-38146705 chr19:38146752-38146761
27	ELF1	chr19:38146827-38147199	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:38145969-38147172	A549	lung:	n/a	n/a
29	POLR2A	chr19:38145482-38146938	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr19:38146653-38147218	GM12878	blood:	n/a	n/a
31	GATA2	chr19:38145898-38147392	SH-SY5Y	brain:	n/a	n/a
32	TAF1	chr19:38145639-38147300	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:38146636-38147187	A549	lung:	n/a	n/a
34	POU2F2	chr19:38146665-38147287	GM12878	blood:	n/a	chr19:38146696-38146708
35	UBTF	chr19:38145491-38147030	K562	blood:	n/a	n/a
36	BHLHE40	chr19:38146164-38147269	HepG2	liver:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
37	RAD21	chr19:38146864-38147269	HepG2	liver:	n/a	chr19:38147033-38147046 chr19:38147128-38147141
38	POLR2A	chr19:38146727-38147221	H1-hESC	embryonic stem cell:	n/a	n/a
39	CHD2	chr19:38146063-38147264	HepG2	liver:	n/a	chr19:38146694-38146704
40	CEBPB	chr19:38146031-38147033	Hela-S3	cervix:	n/a	n/a
41	REST	chr19:38146104-38147547	H1-neurons	neurons:	n/a	chr19:38146308-38146321 chr19:38146695-38146708
42	POLR2A	chr19:38146656-38147250	GM12891	blood:	n/a	n/a
43	ZKSCAN1	chr19:38145626-38147205	Hela-S3	cervix:	n/a	chr19:38146327-38146340
44	BHLHE40	chr19:38145729-38147344	K562	blood:	n/a	chr19:38146433-38146449 chr19:38146999-38147015
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.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38146906-38146956	PANC-1	pancreas:	n/a
2	chr19:38146906-38146956	GM12878	blood:	n/a
3	chr19:38146906-38146956	AG04450	lung:	fetal
4	chr19:38146906-38146956	AG09309	skin:	n/a
5	chr19:38146906-38146956	HAEpiC	amniotic membrane:	n/a
6	chr19:38146906-38146956	SKMC	muscle:	n/a
7	chr19:38146906-38146956	IMR90	lung:	fetal
8	chr19:38146906-38146956	HCPEpiC	choroid plexus:	n/a
9	chr19:38146906-38146956	HepG2	liver:	n/a
10	chr19:38146906-38146956	SK-N-SH	brain:	n/a
11	chr19:38146906-38146956	HL-60	blood:	n/a
12	chr19:38146906-38146956	NH-A	brain:	n/a
13	chr19:38146906-38146956	H1-hESC	embryonic stem cell:	embryo
14	chr19:38146906-38146956	Jurkat	blood:	n/a
15	chr19:38146906-38146956	SK-N-SH_RA	brain:	n/a
16	chr19:38146906-38146956	AoSMC	blood vessel:	n/a
17	chr19:38146906-38146956	GM06990	blood:	n/a
18	chr19:38146906-38146956	NHDF-neo	bronchial:	n/a
19	chr19:38146906-38146956	K562	blood:	n/a
20	chr19:38146906-38146956	PrEC	prostate:	n/a
21	chr19:38146906-38146956	BJ	skin:	n/a
22	chr19:38146906-38146956	HUVEC	blood vessel:	n/a
23	chr19:38146906-38146956	U87	brain:	n/a
24	chr19:38146906-38146956	HRE	kidney:	n/a
25	chr19:38146906-38146956	SAEC	small airway:	n/a
26	chr19:38146906-38146956	HEEpiC	esophagus:	n/a
27	chr19:38146906-38146956	HCF	heart:	n/a
28	chr19:38146906-38146956	HIPEpiC	eye:	n/a
29	chr19:38146906-38146956	HCM	heart:	n/a
30	chr19:38146906-38146956	GM12891	blood:	n/a
31	chr19:38146906-38146956	GM12892	blood:	n/a
32	chr19:38146906-38146956	HNPCEpiC	eye:	n/a
33	chr19:38146906-38146956	PFSK-1	brain:	n/a
34	chr19:38146906-38146956	HRCEpiC	kidney:	n/a
35	chr19:38146906-38146956	ProgFib	skin:	n/a
36	chr19:38146906-38146956	Caco-2	colon:	n/a
37	chr19:38146906-38146956	HCT-116	colon:	n/a
38	chr19:38146906-38146956	LNCaP	prostate:	n/a
39	chr19:38146906-38146956	BE2_C	brain:	n/a
40	chr19:38146906-38146956	AG09319	gingival:	n/a
41	chr19:38146906-38146956	HPAEpiC	pulmonary alveolar:	n/a
42	chr19:38146906-38146956	NHBE	bronchial:	n/a
43	chr19:38146906-38146956	AG10803	skin:	n/a
44	chr19:38146906-38146956	CMK	blood:	n/a
45	chr19:38146906-38146956	HEK293	kidney:	embryo
46	chr19:38146906-38146956	NT2-D1	testis:	n/a
47	chr19:38146906-38146956	T-47D	breast:	n/a
48	chr19:38146906-38146956	SK-N-MC	brain:	n/a
49	chr19:38146906-38146956	AG04449	skin:	fetal
50	chr19:38146906-38146956	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38145174..38146985-chr19:38184008..38186251,2	MCF-7	breast:
2	chr19:38085961..38087829-chr19:38145172..38147580,2	K562	blood:
3	chr19:37957663..37960695-chr19:38143642..38147199,3	MCF-7	breast:
4	chr19:37958940..37961916-chr19:38146231..38147953,2	K562	blood:

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

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10445548	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.86[ASN][1000 genomes]
rs2291001	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.98[EUR][1000 genomes]
rs57943942	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62108291	0.83[EUR][1000 genomes]
rs62108306	0.82[EUR][1000 genomes]
rs7245855	0.86[ASN][1000 genomes]
rs7259272	0.82[EUR][1000 genomes]
rs73031330	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	0.96[AMR][1000 genomes];0.98[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1871196	ZNF781	cis	Thyroid	GTEx
rs1871196	AC012309.5	cis	Esophagus Mucosa	GTEx
rs1871196	AC012309.5	cis	Esophagus Muscularis	GTEx
rs1871196	AC012309.5	cis	Thyroid	GTEx
rs1871196	AC012309.5	cis	Muscle Skeletal	GTEx
rs1871196	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs1871196	AC012309.5	cis	Artery Tibial	GTEx
rs1871196	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs1871196	AC012309.5	cis	Heart Left Ventricle	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	chr19:38144400-38147600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38144600-38147000	Active TSS	A549	lung
5	chr19:38144600-38147200	Active TSS	Fetal Kidney	kidney
6	chr19:38144600-38147400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:38144600-38147400	Active TSS	NHDF-Ad	bronchial
8	chr19:38144600-38147600	Active TSS	Fetal Stomach	stomach
9	chr19:38144600-38147600	Active TSS	Hela-S3	cervix
10	chr19:38144600-38147600	Active TSS	NHLF	lung
11	chr19:38144800-38147200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:38144800-38147200	Active TSS	Fetal Thymus	thymus
13	chr19:38144800-38147400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:38144800-38147400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:38144800-38147400	Active TSS	Left Ventricle	heart
16	chr19:38144800-38147600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:38144800-38147600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:38144800-38147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:38144800-38147600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:38144800-38147600	Active TSS	Fetal Muscle Trunk	muscle
21	chr19:38145000-38147000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:38145000-38147000	Active TSS	Right Ventricle	heart
23	chr19:38145000-38147000	Active TSS	Stomach Smooth Muscle	stomach
24	chr19:38145000-38147200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:38145000-38147200	Active TSS	Muscle Satellite Cultured Cells	--
26	chr19:38145000-38147200	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr19:38145000-38147200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:38145000-38147200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:38145000-38147400	Active TSS	Ovary	ovary
30	chr19:38145000-38147400	Active TSS	Right Atrium	heart
31	chr19:38145000-38147600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr19:38145000-38147600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr19:38145000-38147600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:38145000-38147600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:38145000-38147600	Active TSS	Fetal Intestine Large	intestine
36	chr19:38145000-38147600	Active TSS	Psoas Muscle	Psoas
37	chr19:38145000-38147600	Active TSS	HSMM	muscle
38	chr19:38145000-38147600	Active TSS	HSMMtube	muscle
39	chr19:38145000-38147800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:38145200-38147000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38145200-38147000	Active TSS	Placenta	Placenta
42	chr19:38145200-38147200	Active TSS	Colon Smooth Muscle	Colon
43	chr19:38145200-38147200	Active TSS	Fetal Lung	lung
44	chr19:38145200-38147200	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr19:38145200-38147200	Active TSS	Thymus	Thymus
46	chr19:38145200-38147200	Active TSS	Dnd41	blood
47	chr19:38145200-38147200	Active TSS	NHEK	skin
48	chr19:38145200-38147400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr19:38145200-38147400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:38145200-38147400	Active TSS	Aorta	Aorta

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