Variant report

Variant	rs28688205
Chromosome Location	chr19:21474935-21474936
allele	C/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	POLR2A	chr19:21474922-21475082	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:21474836-21475147	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:21474773-21475176	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:21474768-21474979	K562	blood:	n/a	n/a
5	POLR2A	chr19:21474860-21474956	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:21474767-21475137	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:21474872-21475144	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
VN1R83P	TF binding region

Extended variants
information (count: 116 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10854043	0.91[EUR][1000 genomes]
rs11085441	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11085443	0.81[ASN][1000 genomes]
rs11085447	0.83[EUR][1000 genomes]
rs1142653	0.91[EUR][1000 genomes]
rs11669588	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11673304	0.81[EUR][1000 genomes]
rs11882553	0.84[EUR][1000 genomes]
rs12459702	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12461384	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12462022	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12610331	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12971736	0.88[EUR][1000 genomes]
rs12972339	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972580	0.89[EUR][1000 genomes]
rs12972601	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12974735	0.90[EUR][1000 genomes]
rs12975081	0.91[EUR][1000 genomes]
rs12975464	0.91[EUR][1000 genomes]
rs12978116	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12980097	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12981564	0.91[EUR][1000 genomes]
rs12981735	0.91[EUR][1000 genomes]
rs12981775	0.91[EUR][1000 genomes]
rs12981777	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12982162	0.91[EUR][1000 genomes]
rs12982282	0.91[EUR][1000 genomes]
rs12982346	0.89[EUR][1000 genomes]
rs12983426	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12984300	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12984871	0.88[EUR][1000 genomes]
rs1781873	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1932088	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1963531	0.90[EUR][1000 genomes]
rs1963532	0.88[EUR][1000 genomes]
rs2012013	0.91[EUR][1000 genomes]
rs2012038	0.91[EUR][1000 genomes]
rs2061917	0.91[EUR][1000 genomes]
rs2061918	0.90[EUR][1000 genomes]
rs2061919	0.91[EUR][1000 genomes]
rs2086317	0.91[EUR][1000 genomes]
rs2086318	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2086320	0.88[EUR][1000 genomes]
rs2088762	0.87[EUR][1000 genomes]
rs2102072	0.87[EUR][1000 genomes]
rs2127404	0.89[EUR][1000 genomes]
rs2127405	0.89[EUR][1000 genomes]
rs2127406	0.89[EUR][1000 genomes]
rs2127407	0.88[EUR][1000 genomes]
rs2127408	0.88[EUR][1000 genomes]
rs2170024	0.87[EUR][1000 genomes]
rs2170025	0.88[EUR][1000 genomes]
rs2219840	0.91[EUR][1000 genomes]
rs2358982	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2358983	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2358985	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2358986	0.89[EUR][1000 genomes]
rs2358988	0.89[EUR][1000 genomes]
rs2358989	0.88[EUR][1000 genomes]
rs2358990	0.89[EUR][1000 genomes]
rs2358991	0.88[EUR][1000 genomes]
rs2358992	0.88[EUR][1000 genomes]
rs2434997	0.88[EUR][1000 genomes]
rs279813	0.89[ASN][1000 genomes]
rs2884601	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2914638	0.91[EUR][1000 genomes]
rs2968025	0.84[EUR][1000 genomes]
rs35580411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4315457	0.91[EUR][1000 genomes]
rs4438422	0.91[EUR][1000 genomes]
rs4525621	0.83[EUR][1000 genomes]
rs4566304	0.91[EUR][1000 genomes]
rs6511222	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511229	0.91[EUR][1000 genomes]
rs6511231	0.89[EUR][1000 genomes]
rs6511232	0.89[EUR][1000 genomes]
rs6511233	0.86[EUR][1000 genomes]
rs7245920	0.89[EUR][1000 genomes]
rs7247411	0.88[EUR][1000 genomes]
rs7248601	0.83[EUR][1000 genomes]
rs7252261	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253178	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7256361	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7257580	0.83[EUR][1000 genomes]
rs7258335	0.89[EUR][1000 genomes]
rs7260369	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508030	0.88[EUR][1000 genomes]
rs7508044	0.84[EUR][1000 genomes]
rs7508045	0.84[EUR][1000 genomes]
rs7508072	0.82[EUR][1000 genomes]
rs7508087	0.84[EUR][1000 genomes]
rs7508092	0.89[EUR][1000 genomes]
rs7508104	0.86[EUR][1000 genomes]
rs7508671	0.90[EUR][1000 genomes]
rs8099940	0.88[EUR][1000 genomes]
rs8103325	0.89[EUR][1000 genomes]
rs8103459	0.89[EUR][1000 genomes]
rs8103908	0.89[EUR][1000 genomes]
rs8104017	0.91[EUR][1000 genomes]
rs8110690	0.88[EUR][1000 genomes]
rs8110842	0.88[EUR][1000 genomes]
rs8110967	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8112059	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8112583	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs28688205	RP11-678G14.2	cis	lung	GTEx
rs28688205	CTD-2561J22.5	cis	lung	GTEx
rs28688205	RP11-678G14.2	cis	Whole Blood	GTEx
rs28688205	RP11-678G14.3	cis	Muscle Skeletal	GTEx
rs28688205	CTD-2561J22.5	cis	Skin Sun Exposed Lower leg	GTEx
rs28688205	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28688205	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs28688205	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs28688205	RP11-678G14.2	cis	Thyroid	GTEx
rs28688205	RP11-678G14.2	cis	Artery Tibial	GTEx
rs28688205	RP11-678G14.2	cis	Skin Sun Exposed Lower leg	GTEx
rs28688205	LINC00664	cis	Adipose Subcutaneous	GTEx
rs28688205	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs28688205	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs28688205	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs28688205	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs28688205	CTD-2561J22.5	cis	Nerve Tibial	GTEx
rs28688205	ZNF429	cis	Muscle Skeletal	GTEx
rs28688205	RP11-678G14.2	cis	Nerve Tibial	GTEx
rs28688205	CTD-2561J22.5	cis	Esophagus Muscularis	GTEx
rs28688205	ZNF429	cis	Whole Blood	GTEx
rs28688205	CTD-2561J22.5	cis	Stomach	GTEx
rs28688205	RP11-678G14.3	cis	Whole Blood	GTEx
rs28688205	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs28688205	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs28688205	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs28688205	CTD-2561J22.5	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21465400-21484600	ZNF genes & repeats	Liver	Liver
3	chr19:21467200-21489600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:21470600-21484200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:21471200-21479800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr19:21471600-21479800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:21472000-21476400	Weak transcription	Osteobl	bone
8	chr19:21472000-21481800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:21472200-21487600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:21472200-21490400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:21472400-21475200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:21472800-21475800	Weak transcription	HSMM	muscle
13	chr19:21473000-21476200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:21473200-21475800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:21473200-21476000	Weak transcription	Psoas Muscle	Psoas
16	chr19:21473600-21479400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:21473600-21479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:21473600-21487200	Weak transcription	Right Ventricle	heart
19	chr19:21473800-21475200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:21473800-21476600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:21473800-21479600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
23	chr19:21474000-21478800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:21474000-21479200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
25	chr19:21474000-21481600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:21474000-21490600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:21474200-21475000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr19:21474200-21475200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:21474200-21475200	Strong transcription	HSMMtube	muscle
30	chr19:21474200-21475600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:21474200-21475800	Weak transcription	Fetal Kidney	kidney
32	chr19:21474200-21478200	ZNF genes & repeats	Fetal Brain Female	brain
33	chr19:21474200-21478600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr19:21474200-21479600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:21474200-21480800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:21474200-21482000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:21474400-21475200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:21474400-21475200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:21474400-21475200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:21474400-21475200	ZNF genes & repeats	Aorta	Aorta
41	chr19:21474400-21475200	ZNF genes & repeats	Fetal Intestine Large	intestine
42	chr19:21474400-21475200	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr19:21474400-21475200	ZNF genes & repeats	Left Ventricle	heart
44	chr19:21474400-21475200	Weak transcription	Dnd41	blood
45	chr19:21474400-21476000	Weak transcription	Brain Anterior Caudate	brain
46	chr19:21474400-21476000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:21474400-21477400	Strong transcription	NH-A	brain
48	chr19:21474400-21478000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:21474600-21475000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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