Variant report

Variant	rs7259541
Chromosome Location	chr19:40785779-40785780
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	ZNF263	chr19:40785485-40787027	HEK293-T-REx	kidney:	n/a	n/a
2	ELF1	chr19:40784800-40786773	GM12878	blood:	n/a	chr19:40785706-40785719
3	REST	chr19:40784619-40787303	PANC-1	pancreas:	n/a	chr19:40785994-40786004 chr19:40785201-40785214 chr19:40787050-40787063 chr19:40786402-40786415 chr19:40784931-40784941 chr19:40787050-40787063
4	POLR2A	chr19:40785650-40786251	K562	blood:	n/a	n/a
5	ELF1	chr19:40785495-40785887	K562	blood:	n/a	chr19:40785706-40785719
6	POLR2A	chr19:40781762-40793937	PANC-1	pancreas:	n/a	n/a
7	ZNF143	chr19:40785740-40785937	K562	blood:	n/a	n/a
8	POLR2A	chr19:40785547-40787214	K562	blood:	n/a	n/a
9	POLR2A	chr19:40785526-40787211	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40768260..40771807-chr19:40783478..40786593,4	K562	blood:
2	chr19:40783887..40786272-chr19:41107076..41108731,2	K562	blood:
3	chr19:40776468..40779839-chr19:40784717..40787633,5	MCF-7	breast:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000205041	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11083554	0.81[JPT][hapmap]
rs12151335	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12460555	0.91[JPT][hapmap]
rs16974196	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304186	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2368575	0.85[JPT][hapmap]
rs33933140	0.86[JPT][hapmap]
rs34894858	0.86[JPT][hapmap]
rs3745195	0.85[JPT][hapmap]
rs3746006	1.00[ASW][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4490097	0.85[JPT][hapmap]
rs4502340	0.85[JPT][hapmap]
rs7507651	0.85[JPT][hapmap]
rs890773	0.85[JPT][hapmap]
rs892117	0.86[JPT][hapmap]
rs9636120	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1057052	chr19:40776128-40789766	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	esv1797453	chr19:40780963-40786797	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7259541	TMEM91	cis	parietal	SCAN
rs7259541	MAP3K10	cis	brain	BrainEAC
rs7259541	PSG8	cis	cerebellum	SCAN
rs7259541	GALNTL1	trans	cerebellum	SCAN
rs7259541	ARHGEF1	cis	cerebellum	SCAN
rs7259541	APOC4	cis	cerebellum	SCAN
rs7259541	ZNF428	cis	parietal	SCAN
rs7259541	RABAC1	cis	cerebellum	SCAN
rs7259541	DMRTC2	cis	parietal	SCAN
rs7259541	PLAUR	cis	cerebellum	SCAN
rs7259541	PTGIR	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
2	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
6	chr19:40771400-40789400	Weak transcription	HUVEC	blood vessel
7	chr19:40771600-40786000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:40776000-40787400	Weak transcription	A549	lung
9	chr19:40776600-40785800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:40778000-40786400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:40778800-40786200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:40778800-40787600	Weak transcription	Hela-S3	cervix
13	chr19:40779000-40786800	Weak transcription	Dnd41	blood
14	chr19:40779400-40789600	Enhancers	Left Ventricle	heart
15	chr19:40779800-40789800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:40780600-40786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:40781000-40785800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:40781000-40787800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:40781200-40786000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:40781400-40788000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:40781400-40788000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:40781600-40785800	Enhancers	K562	blood
23	chr19:40781600-40787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:40782200-40789400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:40782800-40785800	Enhancers	Liver	Liver
26	chr19:40782800-40786800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr19:40783000-40788200	Enhancers	Pancreas	Pancrea
28	chr19:40783000-40789600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr19:40783200-40786000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:40783200-40787000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:40783200-40787400	Enhancers	Fetal Intestine Large	intestine
32	chr19:40783200-40787600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:40783200-40788200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr19:40783200-40789200	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:40783400-40785800	Enhancers	Stomach Mucosa	stomach
36	chr19:40783400-40786600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:40783400-40787400	Enhancers	Lung	lung
38	chr19:40783400-40788000	Enhancers	Brain Anterior Caudate	brain
39	chr19:40783400-40788400	Enhancers	Brain Substantia Nigra	brain
40	chr19:40783400-40790000	Enhancers	Right Atrium	heart
41	chr19:40783600-40785800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:40783600-40786000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr19:40783600-40786000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr19:40783600-40787000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:40783600-40787000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr19:40783600-40787200	Enhancers	Placenta	Placenta
47	chr19:40783600-40787400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:40783600-40787400	Enhancers	Fetal Heart	heart
49	chr19:40783600-40788000	Enhancers	Brain Angular Gyrus	brain
50	chr19:40783800-40785800	Enhancers	Fetal Brain Male	brain

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