Variant report

Variant	rs7250408
Chromosome Location	chr19:40333971-40333972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:40333920-40334070	AG09319	gingival:	n/a	n/a
2	CTCF	chr19:40333900-40334050	HEK293	kidney:	n/a	n/a
3	CTCF	chr19:40333920-40334070	HPF	lung:	n/a	n/a
4	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:40333638-40334036	PFSK-1	brain:	n/a	n/a
6	CTCF	chr19:40333900-40334050	HCM	heart:	n/a	n/a
7	SIN3AK20	chr19:40332892-40340524	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr19:40333840-40333990	AG09319	gingival:	n/a	n/a
9	CTCF	chr19:40333860-40334010	HBMEC	blood vessel:	n/a	n/a
10	CTCF	chr19:40333940-40334090	AG04450	lung:	n/a	n/a
11	POLR2A	chr19:40333780-40334173	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr19:40332912-40334212	A549	lung:	n/a	n/a
13	MAX	chr19:40333328-40334005	K562	blood:	n/a	chr19:40333615-40333625

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40282440..40284866-chr19:40332192..40334772,3	K562	blood:
2	chr19:40332447..40334758-chr19:40335345..40337570,4	MCF-7	breast:
3	chr19:40327506..40332289-chr19:40333216..40337866,9	MCF-7	breast:
4	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
5	chr19:40255355..40257924-chr19:40332588..40334816,2	MCF-7	breast:
6	chr19:40245446..40248757-chr19:40332343..40336010,3	MCF-7	breast:
7	chr19:40333922..40335627-chr19:40352940..40355252,2	K562	blood:
8	chr19:40332530..40335412-chr19:40475463..40477228,2	MCF-7	breast:
9	chr19:40163210..40165073-chr19:40333318..40334922,2	MCF-7	breast:

No data

Variant related genes	Relation type
FBL	TF binding region
ENSG00000105204	Chromatin interaction
ENSG00000013275	Chromatin interaction
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1001974	0.82[CHB][hapmap]
rs10416495	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10422280	0.82[GIH][hapmap]
rs11880094	0.82[GIH][hapmap]
rs11881344	0.94[ASN][1000 genomes]
rs12459589	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs12975624	0.89[GIH][hapmap];0.81[MEX][hapmap]
rs17709688	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2072290	0.82[GIH][hapmap]
rs2354471	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs3810383	0.82[GIH][hapmap]
rs4802061	0.82[CHB][hapmap]
rs56047603	0.89[EUR][1000 genomes]
rs616650	0.84[GIH][hapmap]
rs718066	0.82[GIH][hapmap]
rs7247063	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs7253739	0.82[GIH][hapmap]
rs7259470	0.82[CHB][hapmap];0.91[GIH][hapmap]
rs7507534	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7250408	CNFN	cis	cerebellum	SCAN
rs7250408	MARK4	cis	cerebellum	SCAN
rs7250408	NPAS1	cis	cerebellum	SCAN
rs7250408	BCAM	cis	parietal	SCAN
rs7250408	ERF	cis	parietal	SCAN
rs7250408	PHLDB3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40324800-40336000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:40325400-40334800	Weak transcription	Fetal Brain Male	brain
3	chr19:40329600-40335200	Weak transcription	Fetal Kidney	kidney
4	chr19:40329800-40335800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:40330000-40334800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:40330400-40334800	Weak transcription	NH-A	brain
7	chr19:40330800-40334800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:40330800-40334800	Weak transcription	Brain Angular Gyrus	brain
9	chr19:40330800-40335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:40330800-40335600	Weak transcription	Esophagus	oesophagus
11	chr19:40331000-40334400	Weak transcription	Primary B cells from cord blood	blood
12	chr19:40331000-40334800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:40331000-40334800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:40331000-40334800	Weak transcription	Gastric	stomach
15	chr19:40331000-40334800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:40331000-40334800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:40331000-40335000	Weak transcription	Brain Anterior Caudate	brain
18	chr19:40331000-40335200	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:40331000-40335400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:40331200-40334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:40331200-40334800	Weak transcription	Brain Germinal Matrix	brain
22	chr19:40331200-40334800	Weak transcription	Brain Substantia Nigra	brain
23	chr19:40331200-40335000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:40331400-40334400	Weak transcription	Thymus	Thymus
25	chr19:40331400-40334800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:40331400-40335200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:40331400-40335600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:40331400-40335600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr19:40331400-40335600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr19:40331400-40335800	Weak transcription	Colonic Mucosa	Colon
31	chr19:40331600-40334800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr19:40331600-40335200	Weak transcription	Fetal Brain Female	brain
33	chr19:40332000-40334400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr19:40332000-40334800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:40332200-40334400	Enhancers	HepG2	liver
36	chr19:40332200-40334800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:40332200-40334800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:40332200-40335400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:40332200-40335600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:40332200-40336000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr19:40332200-40336000	Enhancers	Liver	Liver
42	chr19:40332400-40334000	Genic enhancers	A549	lung
43	chr19:40332400-40334200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:40332400-40334600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:40332400-40336000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr19:40332600-40334800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:40332600-40334800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:40332600-40335400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:40332600-40335600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr19:40333000-40334000	Enhancers	HSMMtube	muscle

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