Variant report

Variant	rs7248885
Chromosome Location	chr19:19753292-19753293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr19:19753142-19753712	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:19753278-19754851	GM12891	blood:	n/a	n/a
3	CTCF	chr19:19753220-19753370	GM12875	blood:	n/a	n/a
4	POLR2A	chr19:19753077-19755139	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:19753079-19755081	GM12892	blood:	n/a	n/a
6	CTCF	chr19:19753281-19753479	GM19238	blood:	n/a	n/a
7	POLR2A	chr19:19753250-19755040	GM18951	blood:	n/a	n/a
8	POLR2A	chr19:19753227-19755267	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:19753159-19754994	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:19753278-19755063	GM12878	blood:	n/a	n/a
11	CTCF	chr19:19753260-19753410	GM12870	blood:	n/a	n/a
12	POLR2A	chr19:19753228-19754960	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:19752168-19755059	GM12878	blood:	n/a	n/a
14	CTCF	chr19:19753269-19753475	GM12892	blood:	n/a	n/a
15	CTCF	chr19:19753280-19753430	GM12867	blood:	n/a	n/a
16	EBF1	chr19:19753257-19753913	GM12878	blood:	n/a	chr19:19753426-19753437
17	RUNX3	chr19:19753184-19755046	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:19753040-19755067	GM12892	blood:	n/a	n/a
19	CTCF	chr19:19753280-19753430	HEEpiC	esophagus:	n/a	n/a
20	POLR2A	chr19:19753156-19755303	GM12891	blood:	n/a	n/a
21	CTCF	chr19:19753285-19753458	GM12878	blood:	n/a	n/a
22	CTCF	chr19:19753280-19753430	GM06990	blood:	n/a	n/a
23	NFIC	chr19:19753219-19754381	GM12878	blood:	n/a	n/a
24	CTCF	chr19:19753276-19753551	GM12878	blood:	n/a	n/a
25	CTCF	chr19:19753260-19753410	GM12875	blood:	n/a	n/a
26	POLR2A	chr19:19753242-19754992	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:19753264-19753781	GM12891	blood:	n/a	n/a
28	PML	chr19:19753179-19755120	GM12878	blood:	n/a	chr19:19753635-19753643
29	MXI1	chr19:19753212-19755007	GM12878	blood:	n/a	chr19:19754710-19754719
30	RUNX3	chr19:19753205-19755079	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:19753248-19755082	GM18505	blood:	n/a	n/a
32	POLR2A	chr19:19753245-19755403	HL-60	blood:	n/a	n/a
33	POLR2A	chr19:19753277-19755150	HL-60	blood:	n/a	n/a
34	POLR2A	chr19:19752547-19754995	GM12878	blood:	n/a	n/a
35	MAZ	chr19:19753176-19754918	GM12878	blood:	n/a	chr19:19754681-19754691
36	CTCF	chr19:19753280-19753430	GM12873	blood:	n/a	n/a
37	POLR2A	chr19:19753193-19755034	GM12878	blood:	n/a	n/a
38	ELF1	chr19:19753200-19755088	GM12878	blood:	n/a	chr19:19754073-19754084
39	POLR2A	chr19:19753241-19755069	GM12891	blood:	n/a	n/a
40	CTCF	chr19:19753280-19753430	NB4	blood:	n/a	n/a
41	CTCF	chr19:19753260-19753410	GM12864	blood:	n/a	n/a
42	TAF1	chr19:19753270-19754164	GM12878	blood:	n/a	n/a
43	CHD2	chr19:19753243-19754941	GM12878	blood:	n/a	n/a
44	MXI1	chr19:19753050-19755147	SK-N-SH	brain:	n/a	chr19:19754710-19754719
45	STAT3	chr19:19753179-19753298	MCF10A-Er-Src	breast:	n/a	n/a
46	MTA3	chr19:19752998-19755384	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:19753227-19754766	GM12892	blood:	n/a	n/a
48	CTCF	chr19:19753283-19753475	GM12891	blood:	n/a	n/a
49	RAD21	chr19:19753178-19755189	SK-N-SH	brain:	n/a	chr19:19754824-19754837 chr19:19754825-19754835 chr19:19754963-19754976 chr19:19754821-19754840

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19751893..19756920-chr19:19758472..19762276,9	K562	blood:
2	chr19:19736821..19742043-chr19:19751528..19755876,8	MCF-7	breast:
3	chr19:19649879..19653588-chr19:19753029..19755939,4	K562	blood:
4	chr19:19747528..19750723-chr19:19750885..19753735,4	MCF-7	breast:
5	chr19:19751259..19758144-chr19:19770384..19776332,14	K562	blood:
6	chr19:19753162..19754752-chr19:19769276..19770855,2	MCF-7	breast:
7	chr19:19752450..19756333-chr19:19763709..19769200,7	K562	blood:
8	chr19:19729600..19731507-chr19:19752222..19754293,3	K562	blood:
9	chr19:19751259..19757786-chr19:19771999..19776232,8	K562	blood:
10	chr19:19752883..19756107-chr19:19759212..19764518,8	MCF-7	breast:
11	chr19:19625550..19627956-chr19:19752305..19756076,5	MCF-7	breast:
12	chr19:19752144..19756505-chr19:19773208..19775858,7	MCF-7	breast:
13	chr19:19637478..19643205-chr19:19752988..19755970,5	MCF-7	breast:
14	chr19:19647280..19649688-chr19:19752870..19754432,2	MCF-7	breast:
15	chr19:19650697..19653588-chr19:19753029..19754860,3	K562	blood:

No data

Variant related genes	Relation type
GMIP	TF binding region
ENSG00000064547	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000105717	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000105726	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10407283	0.81[JPT][hapmap]
rs10416924	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs10417097	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs1054685	0.87[CEU][hapmap];0.80[TSI][hapmap]
rs11880888	0.87[CEU][hapmap]
rs6511040	0.83[CEU][hapmap]
rs6511046	0.91[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7248200	0.81[JPT][hapmap]
rs8113221	0.83[CEU][hapmap]
rs873870	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7248885	SLC27A1	cis	cerebellum	SCAN
rs7248885	HAUS8	cis	parietal	SCAN
rs7248885	KCNK9	trans	parietal	SCAN
rs7248885	GATAD2A	cis	parietal	SCAN
rs7248885	TNFAIP1	trans	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19739800-19753400	Weak transcription	Small Intestine	intestine
2	chr19:19739800-19753400	Weak transcription	HMEC	breast
3	chr19:19739800-19753600	Weak transcription	Brain Angular Gyrus	brain
4	chr19:19739800-19753600	Weak transcription	Brain Substantia Nigra	brain
5	chr19:19739800-19753600	Weak transcription	Left Ventricle	heart
6	chr19:19739800-19753600	Weak transcription	Right Atrium	heart
7	chr19:19740000-19753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19740000-19753400	Weak transcription	Brain Anterior Caudate	brain
9	chr19:19740000-19753600	Weak transcription	Fetal Kidney	kidney
10	chr19:19745600-19753400	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:19745600-19753400	Weak transcription	HUVEC	blood vessel
12	chr19:19745800-19753400	Weak transcription	A549	lung
13	chr19:19745800-19753600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:19746200-19753400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr19:19746400-19753600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:19746600-19753400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:19746600-19753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:19746600-19753400	Weak transcription	HSMMtube	muscle
19	chr19:19746600-19753600	Weak transcription	Fetal Intestine Large	intestine
20	chr19:19746600-19753600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:19746600-19753800	Weak transcription	Aorta	Aorta
22	chr19:19746600-19753800	Weak transcription	Ovary	ovary
23	chr19:19746800-19753400	Weak transcription	Fetal Lung	lung
24	chr19:19746800-19753400	Weak transcription	HSMM	muscle
25	chr19:19747800-19753400	Weak transcription	NHLF	lung
26	chr19:19748000-19753400	Weak transcription	NH-A	brain
27	chr19:19748000-19753600	Weak transcription	Liver	Liver
28	chr19:19748200-19753400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:19748200-19753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:19748600-19753400	Weak transcription	Placenta	Placenta
31	chr19:19748600-19753600	Weak transcription	Right Ventricle	heart
32	chr19:19748800-19753600	Weak transcription	Fetal Heart	heart
33	chr19:19749000-19753400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr19:19749200-19753400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:19749400-19753400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:19749600-19753400	Weak transcription	Gastric	stomach
37	chr19:19751400-19753400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:19751400-19753400	Weak transcription	Fetal Intestine Small	intestine
39	chr19:19751400-19753400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:19752600-19753400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
41	chr19:19752600-19753600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr19:19752600-19754400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:19752800-19753400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:19752800-19753400	Enhancers	Stomach Mucosa	stomach
45	chr19:19753000-19753400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr19:19753000-19753400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:19753000-19753400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr19:19753000-19753400	Weak transcription	Fetal Stomach	stomach
49	chr19:19753000-19753400	Weak transcription	Spleen	Spleen
50	chr19:19753000-19753400	Flanking Active TSS	GM12878-XiMat	blood

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