Variant report

Variant	rs17754589
Chromosome Location	chr8:11625808-11625809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:11625695-11626321	GM12892	blood:	n/a	n/a
2	RUNX3	chr8:11625576-11626330	GM12878	blood:	n/a	n/a
3	CTCF	chr8:11625681-11625896	GM19238	blood:	n/a	n/a
4	RELA	chr8:11625731-11626406	GM19099	blood:	n/a	n/a
5	POLR2A	chr8:11625781-11627973	GM19099	blood:	n/a	n/a
6	RELA	chr8:11625716-11626400	GM15510	blood:	n/a	n/a
7	RUNX3	chr8:11625568-11626334	GM12878	blood:	n/a	n/a
8	RELA	chr8:11625714-11626598	GM12891	blood:	n/a	n/a
9	CTCF	chr8:11625718-11625827	Spleen_OC	spleen:	n/a	n/a
10	POLR2A	chr8:11625715-11626043	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:11625764-11625814	ECC-1	luminal epithelium:	n/a
2	chr8:11625764-11625814	GM06990	blood:	n/a
3	chr8:11625764-11625814	T-47D	breast:	n/a
4	chr8:11625764-11625814	BE2_C	brain:	n/a
5	chr8:11625764-11625814	A549	lung:	n/a
6	chr8:11625764-11625814	ovcar-3	ovarian:	n/a
7	chr8:11625764-11625814	HCT-116	colon:	n/a
8	chr8:11625764-11625814	BJ	skin:	n/a
9	chr8:11625764-11625814	GM12891	blood:	n/a
10	chr8:11625764-11625814	AG09319	gingival:	n/a
11	chr8:11625764-11625814	PrEC	prostate:	n/a
12	chr8:11625764-11625814	NHBE	bronchial:	n/a
13	chr8:11625764-11625814	AG04450	lung:	fetal
14	chr8:11625764-11625814	HUVEC	blood vessel:	n/a
15	chr8:11625764-11625814	NH-A	brain:	n/a
16	chr8:11625764-11625814	HCM	heart:	n/a
17	chr8:11625764-11625814	HAEpiC	amniotic membrane:	n/a
18	chr8:11625764-11625814	HEEpiC	esophagus:	n/a
19	chr8:11625764-11625814	LNCaP	prostate:	n/a
20	chr8:11625764-11625814	SK-N-MC	brain:	n/a
21	chr8:11625764-11625814	SKMC	muscle:	n/a
22	chr8:11625764-11625814	U87	brain:	n/a
23	chr8:11625764-11625814	HRPEpiC	eye:	n/a
24	chr8:11625764-11625814	H1-hESC	embryonic stem cell:	embryo
25	chr8:11625764-11625814	IMR90	lung:	fetal
26	chr8:11625764-11625814	Jurkat	blood:	n/a
27	chr8:11625764-11625814	SK-N-SH_RA	brain:	n/a
28	chr8:11625764-11625814	RPTEC	kidney:	n/a
29	chr8:11625764-11625814	NT2-D1	testis:	n/a
30	chr8:11625764-11625814	NHDF-neo	bronchial:	n/a
31	chr8:11625764-11625814	GM12878	blood:	n/a
32	chr8:11625764-11625814	HIPEpiC	eye:	n/a
33	chr8:11625764-11625814	MCF10A-Er-Src	breast:	n/a
34	chr8:11625764-11625814	HNPCEpiC	eye:	n/a
35	chr8:11625764-11625814	HCPEpiC	choroid plexus:	n/a
36	chr8:11625764-11625814	ProgFib	skin:	n/a
37	chr8:11625764-11625814	CMK	blood:	n/a
38	chr8:11625764-11625814	HL-60	blood:	n/a
39	chr8:11625764-11625814	Hela-S3	cervix:	n/a
40	chr8:11625764-11625814	Caco-2	colon:	n/a
41	chr8:11625764-11625814	PANC-1	pancreas:	n/a
42	chr8:11625764-11625814	GM19239	blood:	n/a
43	chr8:11625764-11625814	HRCEpiC	kidney:	n/a
44	chr8:11625764-11625814	SAEC	small airway:	n/a
45	chr8:11625764-11625814	HPAEpiC	pulmonary alveolar:	n/a
46	chr8:11625764-11625814	GM12892	blood:	n/a
47	chr8:11625764-11625814	Hepatocyte	liver:	n/a
48	chr8:11625764-11625814	NB4	blood:	n/a
49	chr8:11625764-11625814	HepG2	liver:	n/a
50	chr8:11625764-11625814	HEK293	kidney:	embryo

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:11625684..11627765-chr8:11645905..11648269,2	K562	blood:
2	chr8:11625747..11629309-chr8:11658765..11661345,4	K562	blood:
3	chr8:11625432..11628777-chr8:11664764..11667821,4	MCF-7	breast:
4	chr8:11624784..11628111-chr8:11660073..11663416,4	MCF-7	breast:

No data

Variant related genes	Relation type
NEIL2	TF binding region
NEIL2	CpG island
ENSG00000255046	Chromatin interaction
ENSG00000079459	Chromatin interaction
ENSG00000227203	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10098874	1.00[JPT][hapmap]
rs10101195	0.89[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs1047643	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1534862	0.86[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs1883016	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4840581	1.00[JPT][hapmap]
rs55865839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66651545	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67123108	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7000800	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804267	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs804269	1.00[JPT][hapmap]
rs8191511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8191528	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8191534	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8191604	0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8191642	0.83[AMR][1000 genomes]
rs8191649	0.84[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs8191663	0.91[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs904009	0.87[CEU][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription 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	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17754589	XKR6	cis	cerebellum	SCAN
rs17754589	NEIL2	Cis_1M	lymphoblastoid	RTeQTL
rs17754589	PPP1R3B	cis	cerebellum	SCAN
rs17754589	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11615800-11626800	Weak transcription	Left Ventricle	heart
2	chr8:11617000-11626800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:11617400-11626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:11617400-11626400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:11617400-11626800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:11618000-11626000	Weak transcription	Pancreas	Pancrea
7	chr8:11618000-11626800	Weak transcription	Fetal Intestine Large	intestine
8	chr8:11619600-11626800	Weak transcription	Gastric	stomach
9	chr8:11620400-11626600	Weak transcription	Right Ventricle	heart
10	chr8:11621200-11626600	Weak transcription	Fetal Intestine Small	intestine
11	chr8:11622400-11626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:11623400-11626000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr8:11623400-11626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr8:11623400-11626000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:11623400-11626000	Weak transcription	Fetal Thymus	thymus
16	chr8:11623400-11626000	Weak transcription	Right Atrium	heart
17	chr8:11623400-11626400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:11623400-11626600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:11623400-11626600	Weak transcription	Brain Anterior Caudate	brain
20	chr8:11623400-11626600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr8:11623400-11626600	Weak transcription	Brain Substantia Nigra	brain
22	chr8:11623400-11626600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr8:11623400-11626600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr8:11623400-11626800	Weak transcription	Spleen	Spleen
25	chr8:11623600-11626000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:11623600-11626000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr8:11623600-11626000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr8:11623600-11626000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr8:11623600-11626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:11623600-11626000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr8:11623600-11626000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr8:11623600-11626000	Weak transcription	K562	blood
33	chr8:11623600-11626200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr8:11623600-11626400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr8:11623600-11626400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr8:11623600-11626400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr8:11623600-11626400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr8:11623600-11626400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr8:11623600-11626400	Weak transcription	Liver	Liver
40	chr8:11623600-11626400	Weak transcription	Brain Hippocampus Middle	brain
41	chr8:11623600-11626400	Weak transcription	Stomach Mucosa	stomach
42	chr8:11623600-11626600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr8:11623600-11626600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr8:11623600-11626600	Weak transcription	Colon Smooth Muscle	Colon
45	chr8:11623600-11626600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr8:11623600-11626600	Weak transcription	Fetal Brain Male	brain
47	chr8:11623600-11626600	Weak transcription	A549	lung
48	chr8:11623600-11626800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:11623600-11626800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr8:11623600-11626800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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