Variant report

Variant	rs16987295
Chromosome Location	chr19:57020025-57020026
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	NRF1	chr19:57018621-57020372	SK-N-SH	brain:	n/a	chr19:57019014-57019028 chr19:57019208-57019219 chr19:57019011-57019025 chr19:57019016-57019025 chr19:57019210-57019219 chr19:57019208-57019222 chr19:57019014-57019025
2	MXI1	chr19:57018571-57020457	IMR90	lung:	n/a	chr19:57020209-57020218
3	SIN3A	chr19:57018519-57020072	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:57018640-57020092	H1-neurons	neurons:	n/a	n/a
5	REST	chr19:57018371-57020050	H1-neurons	neurons:	n/a	chr19:57018882-57018889
6	POLR2A	chr19:57019048-57020231	IMR90	lung:	n/a	n/a
7	MXI1	chr19:57018355-57020592	SK-N-SH	brain:	n/a	chr19:57020209-57020218
8	MAZ	chr19:57018669-57020086	IMR90	lung:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
9	POLR2A	chr19:57018674-57020096	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:57019659..57020659-chr6:103890104..103890604,2	MCF-7	breast:

Variant related genes	Relation type
ZNF471	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10417966	0.80[YRI][hapmap]
rs10419553	0.80[YRI][hapmap]
rs11084452	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671776	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151254	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12978999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980452	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12981980	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12986047	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs15507	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987303	0.94[CEU][hapmap]
rs16987310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074941	0.83[YRI][hapmap]
rs2074942	0.83[YRI][hapmap]
rs2215151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286422	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869891	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088221	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34269477	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35347939	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35664312	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35908973	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36020383	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36062917	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813142	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4267437	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4570977	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4801334	0.95[YRI][hapmap]
rs61144294	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62123030	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62124070	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66522479	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245557	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246507	1.00[CHB][hapmap]
rs7250075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs960997	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16987295	ZFP28	Cis_1M	lymphoblastoid	RTeQTL
rs16987295	AC007228.11	cis	Esophagus Muscularis	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57018200-57020200	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr19:57018400-57020400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:57018400-57020400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:57018600-57020200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:57018600-57020200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:57018600-57020200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:57018600-57020200	Active TSS	Aorta	Aorta
8	chr19:57018600-57020200	Active TSS	Fetal Muscle Trunk	muscle
9	chr19:57018600-57020400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:57018600-57020400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr19:57018600-57020400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
12	chr19:57018600-57020400	ZNF genes & repeats	Spleen	Spleen
13	chr19:57019400-57020400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:57019600-57020200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
15	chr19:57019600-57020200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:57019600-57020200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr19:57019600-57020200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr19:57019600-57020200	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr19:57019600-57020200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr19:57019600-57020200	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr19:57019600-57020200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:57019600-57020200	Flanking Active TSS	Colonic Mucosa	Colon
23	chr19:57019600-57020200	Flanking Active TSS	Esophagus	oesophagus
24	chr19:57019600-57020200	Flanking Active TSS	Pancreas	Pancrea
25	chr19:57019600-57020200	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr19:57019600-57020200	Flanking Active TSS	HUVEC	blood vessel
27	chr19:57019600-57020400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:57019600-57020400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr19:57019600-57020400	Flanking Active TSS	Liver	Liver
30	chr19:57019600-57020400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr19:57019600-57020400	Flanking Active TSS	NHEK	skin
32	chr19:57019600-57020600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr19:57019600-57020600	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr19:57019800-57020200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:57019800-57020200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:57019800-57020200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr19:57019800-57020200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:57019800-57020200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:57019800-57020200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:57019800-57020200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr19:57019800-57020200	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr19:57019800-57020200	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr19:57019800-57020200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr19:57019800-57020200	Flanking Active TSS	Fetal Heart	heart
45	chr19:57019800-57020200	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr19:57019800-57020200	Flanking Active TSS	Fetal Stomach	stomach
47	chr19:57019800-57020200	Flanking Active TSS	Gastric	stomach
48	chr19:57019800-57020200	Flanking Active TSS	Left Ventricle	heart
49	chr19:57019800-57020200	Flanking Active TSS	Lung	lung
50	chr19:57019800-57020200	Flanking Active TSS	Ovary	ovary

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