Variant report

Variant	rs7250448
Chromosome Location	chr19:36543413-36543414
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr19:36543324-36543622	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36497884..36507784-chr19:36542079..36547610,17	MCF-7	breast:
2	chr19:36543278..36547003-chr19:36629856..36633093,3	MCF-7	breast:
3	chr19:36543201..36546500-chr19:36630161..36633757,3	MCF-7	breast:
4	chr19:36496294..36501686-chr19:36543356..36547257,9	MCF-7	breast:
5	chr19:36502189..36508386-chr19:36540645..36546835,9	MCF-7	breast:

No data

Variant related genes	Relation type
WDR62	TF binding region
ENSG00000267698	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000239382	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10414679	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10418015	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs10420353	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10421966	0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10426582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12462674	0.85[CHB][hapmap]
rs12972490	0.96[ASN][1000 genomes]
rs12972660	0.85[AMR][1000 genomes]
rs12976505	0.98[ASN][1000 genomes]
rs12976812	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12977802	0.91[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs12977814	0.98[ASN][1000 genomes]
rs12978482	0.98[ASN][1000 genomes]
rs12979093	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981654	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1548506	0.87[YRI][hapmap]
rs2023865	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs2051800	0.88[YRI][hapmap]
rs2072606	0.82[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs2075474	0.87[AMR][1000 genomes]
rs34906485	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35875194	0.80[ASN][1000 genomes]
rs3826995	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs4461192	0.85[CHB][hapmap]
rs4805154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4805155	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806252	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4806253	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4806279	0.80[AMR][1000 genomes]
rs4806280	0.82[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs56034793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62109743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71337524	0.94[ASN][1000 genomes]
rs7245762	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7247057	0.86[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs7257383	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs757223	0.88[YRI][hapmap]
rs8100250	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8103569	0.85[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7250448	TEX101	cis	parietal	SCAN
rs7250448	PHLDB3	cis	parietal	SCAN
rs7250448	PSG2	cis	parietal	SCAN
rs7250448	ZNF229	cis	parietal	SCAN
rs7250448	PSG9	cis	cerebellum	SCAN
rs7250448	ZNF573	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
3	chr19:36524200-36543800	Weak transcription	Left Ventricle	heart
4	chr19:36524200-36544000	Weak transcription	Primary B cells from cord blood	blood
5	chr19:36524200-36544400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:36524200-36544400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:36524200-36544400	Weak transcription	Aorta	Aorta
8	chr19:36524400-36543800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:36524400-36544000	Weak transcription	Fetal Lung	lung
10	chr19:36526400-36544200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:36526600-36544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:36526800-36544400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:36527000-36544600	Weak transcription	Gastric	stomach
14	chr19:36528400-36544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:36528600-36543800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr19:36528600-36543800	Weak transcription	Fetal Thymus	thymus
17	chr19:36528600-36544000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:36528600-36544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:36528600-36544400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:36528600-36544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:36530400-36544200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:36530400-36544400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:36530600-36543800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr19:36530600-36544000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:36530600-36544400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:36530800-36543800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:36530800-36543800	Weak transcription	Brain Germinal Matrix	brain
28	chr19:36530800-36543800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:36531000-36543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:36531000-36543800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:36531000-36543800	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:36531000-36544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:36531000-36544000	Weak transcription	Esophagus	oesophagus
34	chr19:36531200-36543800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:36531200-36544000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr19:36531400-36544000	Weak transcription	Spleen	Spleen
37	chr19:36531800-36543600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:36532600-36543800	Weak transcription	Fetal Intestine Large	intestine
39	chr19:36532800-36543600	Weak transcription	Hela-S3	cervix
40	chr19:36533000-36544600	Weak transcription	Lung	lung
41	chr19:36533200-36544200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:36533200-36544400	Weak transcription	Fetal Heart	heart
43	chr19:36533200-36544400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:36533400-36543600	Weak transcription	Fetal Kidney	kidney
45	chr19:36533400-36543600	Weak transcription	HSMMtube	muscle
46	chr19:36533400-36544600	Weak transcription	Ovary	ovary
47	chr19:36533600-36543600	Weak transcription	NHDF-Ad	bronchial
48	chr19:36533800-36544400	Weak transcription	A549	lung
49	chr19:36535200-36544000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:36537000-36543800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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