Variant report

Variant	rs7257809
Chromosome Location	chr19:44528978-44528979
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	chr19:44528964-44529685	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIX5	chr19:44528955-44529883	A549	lung:	n/a	n/a
3	GABPA	chr19:44528881-44529926	A549	lung:	n/a	chr19:44529643-44529652
4	REST	chr19:44528739-44530086	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr19:44528950-44529899	PFSK-1	brain:	n/a	n/a
6	GABPA	chr19:44528950-44529884	SK-N-SH	brain:	n/a	chr19:44529643-44529652
7	HCFC1	chr19:44528678-44529987	Hela-S3	cervix:	n/a	n/a
8	MAX	chr19:44528796-44529874	A549	lung:	n/a	n/a
9	TCF12	chr19:44528874-44529909	A549	lung:	n/a	n/a
10	POLR2A	chr19:44528900-44529894	H1-neurons	neurons:	n/a	n/a
11	MXI1	chr19:44528791-44530560	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44505664..44508645-chr19:44527908..44530282,2	MCF-7	breast:

Variant related genes	Relation type
ZNF222	TF binding region
ENSG00000267022	TF binding region
ENSG00000159882	Chromatin interaction
ENSG00000266921	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11083734	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083735	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083736	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083737	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666432	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12610472	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474061	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1996409	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138823	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2138824	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2176431	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs382197	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3826941	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4239528	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs427608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4299256	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4371266	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4375771	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4444434	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs451388	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs454904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4550576	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4555257	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803668	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803672	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803674	0.91[CHB][hapmap]
rs55798868	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56003307	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56230322	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56250154	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57895932	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62115491	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62119177	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6509135	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6509137	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7251015	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7252213	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255192	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8105003	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8109313	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109615	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8110348	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9646633	0.85[EUR][1000 genomes];0.85[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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7257809	ASPDH	cis	cerebellum	SCAN
rs7257809	ZNF223	cis	Thyroid	GTEx
rs7257809	FUT2	cis	parietal	SCAN
rs7257809	ZNF613	cis	parietal	SCAN
rs7257809	ZNF284	cis	lymphoblastoid	seeQTL
rs7257809	ETFB	cis	parietal	SCAN
rs7257809	C14orf50	trans	parietal	SCAN
rs7257809	EMP3	cis	parietal	SCAN
rs7257809	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs7257809	ZNF223	cis	Nerve Tibial	GTEx
rs7257809	ZNF223	cis	Adipose Subcutaneous	GTEx
rs7257809	OPA3	cis	parietal	SCAN
rs7257809	APOC2	cis	parietal	SCAN
rs7257809	HIF3A	cis	parietal	SCAN
rs7257809	SPHK2	cis	parietal	SCAN
rs7257809	KPTN	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44515400-44529000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:44528400-44529200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:44528800-44529000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr19:44528800-44529000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:44528800-44529000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:44528800-44529000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:44528800-44529000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr19:44528800-44529000	Enhancers	Primary B cells from peripheral blood	blood
9	chr19:44528800-44529000	Enhancers	Primary T cells from cord blood	blood
10	chr19:44528800-44529000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr19:44528800-44529000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr19:44528800-44529000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr19:44528800-44529000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:44528800-44529000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr19:44528800-44529000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:44528800-44529000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:44528800-44529000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:44528800-44529000	Active TSS	Adipose Nuclei	Adipose
19	chr19:44528800-44529000	Enhancers	Colon Smooth Muscle	Colon
20	chr19:44528800-44529000	Active TSS	Duodenum Mucosa	Duodenum
21	chr19:44528800-44529000	Enhancers	Fetal Intestine Small	intestine
22	chr19:44528800-44529000	Enhancers	Fetal Kidney	kidney
23	chr19:44528800-44529000	Enhancers	Fetal Thymus	thymus
24	chr19:44528800-44529000	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:44528800-44529000	Active TSS	GM12878-XiMat	blood
26	chr19:44528800-44529000	Enhancers	HMEC	breast
27	chr19:44528800-44529000	Weak transcription	HSMM	muscle
28	chr19:44528800-44529000	Active TSS	K562	blood
29	chr19:44528800-44529000	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr19:44528800-44529000	Enhancers	NHEK	skin
31	chr19:44528800-44529200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:44528800-44529200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:44528800-44529200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr19:44528800-44529200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:44528800-44529200	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr19:44528800-44529200	ZNF genes & repeats	A549	lung
37	chr19:44528800-44529200	Flanking Active TSS	HepG2	liver
38	chr19:44528800-44529200	Flanking Active TSS	HSMMtube	muscle
39	chr19:44528800-44529400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:44528800-44529400	Flanking Active TSS	Liver	Liver
41	chr19:44528800-44529400	Flanking Active TSS	Dnd41	blood
42	chr19:44528800-44529800	Active TSS	Brain Hippocampus Middle	brain
43	chr19:44528800-44530000	Active TSS	Brain Cingulate Gyrus	brain
44	chr19:44528800-44530000	Active TSS	Brain Substantia Nigra	brain
45	chr19:44528800-44530200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:44528800-44530200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:44528800-44530200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr19:44528800-44530200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr19:44528800-44530400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:44528800-44530400	Active TSS	Rectal Mucosa Donor 29	rectum

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