Variant report

Variant	rs2290526
Chromosome Location	chr8:60032805-60032806
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:60032053-60032963	A549	lung:	n/a	chr8:60032692-60032705
2	RAD21	chr8:60032114-60033273	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr8:60031565-60032927	IMR90	lung:	n/a	chr8:60031868-60031878
4	ZBTB7A	chr8:60032038-60032815	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr8:60026013-60032839	GM12892	blood:	n/a	n/a
6	SIN3A	chr8:60032047-60033207	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr8:60029630-60032925	H1-neurons	neurons:	n/a	chr8:60030756-60030769 chr8:60031242-60031262 chr8:60030645-60030658
8	CTCF	chr8:60032029-60032835	SK-N-SH	brain:	n/a	chr8:60032692-60032705
9	SMC3	chr8:60029628-60033412	SK-N-SH	brain:	n/a	chr8:60030234-60030241
10	ELF1	chr8:60032394-60032807	GM12878	blood:	n/a	n/a
11	CTCF	chr8:60032680-60032830	HAc	cerebellar:	n/a	chr8:60032692-60032705
12	HDAC2	chr8:60032395-60032971	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr8:60029804-60033039	GM18505	blood:	n/a	n/a
14	BACH1	chr8:60032159-60033118	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZBTB7A	chr8:60032022-60032848	ECC-1	luminal epithelium:	n/a	n/a
16	MXI1	chr8:60027222-60033187	SK-N-SH	brain:	n/a	chr8:60030980-60030995

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:60032794-60032844	HPAEpiC	pulmonary alveolar:	n/a
2	chr8:60032794-60032844	HRE	kidney:	n/a
3	chr8:60032794-60032844	NHDF-neo	bronchial:	n/a
4	chr8:60032794-60032844	AoSMC	blood vessel:	n/a
5	chr8:60032794-60032844	RPTEC	kidney:	n/a
6	chr8:60032794-60032844	HUVEC	blood vessel:	n/a
7	chr8:60032794-60032844	BE2_C	brain:	n/a
8	chr8:60032794-60032844	Hepatocyte	liver:	n/a
9	chr8:60032794-60032844	NT2-D1	testis:	n/a
10	chr8:60032794-60032844	ovcar-3	ovarian:	n/a
11	chr8:60032794-60032844	GM06990	blood:	n/a
12	chr8:60032794-60032844	IMR90	lung:	fetal
13	chr8:60032794-60032844	HNPCEpiC	eye:	n/a
14	chr8:60032794-60032844	ECC-1	luminal epithelium:	n/a
15	chr8:60032794-60032844	SKMC	muscle:	n/a
16	chr8:60032794-60032844	HIPEpiC	eye:	n/a
17	chr8:60032794-60032844	HCT-116	colon:	n/a
18	chr8:60032794-60032844	AG10803	skin:	n/a
19	chr8:60032794-60032844	NB4	blood:	n/a
20	chr8:60032794-60032844	Jurkat	blood:	n/a
21	chr8:60032794-60032844	AG09319	gingival:	n/a
22	chr8:60032794-60032844	SK-N-MC	brain:	n/a
23	chr8:60032794-60032844	GM12892	blood:	n/a
24	chr8:60032794-60032844	H1-hESC	embryonic stem cell:	embryo
25	chr8:60032794-60032844	HCPEpiC	choroid plexus:	n/a
26	chr8:60032794-60032844	LNCaP	prostate:	n/a
27	chr8:60032794-60032844	U87	brain:	n/a
28	chr8:60032794-60032844	MCF10A-Er-Src	breast:	n/a
29	chr8:60032794-60032844	SK-N-SH	brain:	n/a
30	chr8:60032794-60032844	HAEpiC	amniotic membrane:	n/a
31	chr8:60032794-60032844	HEEpiC	esophagus:	n/a
32	chr8:60032794-60032844	GM12878	blood:	n/a
33	chr8:60032794-60032844	HMEC	breast:	n/a
34	chr8:60032794-60032844	PrEC	prostate:	n/a
35	chr8:60032794-60032844	NH-A	brain:	n/a
36	chr8:60032794-60032844	K562	blood:	n/a
37	chr8:60032794-60032844	CMK	blood:	n/a
38	chr8:60032794-60032844	BJ	skin:	n/a
39	chr8:60032794-60032844	HEK293	kidney:	embryo
40	chr8:60032794-60032844	Caco-2	colon:	n/a
41	chr8:60032794-60032844	GM12891	blood:	n/a
42	chr8:60032794-60032844	HCF	heart:	n/a
43	chr8:60032794-60032844	AG09309	skin:	n/a
44	chr8:60032794-60032844	HRPEpiC	eye:	n/a
45	chr8:60032794-60032844	HRCEpiC	kidney:	n/a
46	chr8:60032794-60032844	HCM	heart:	n/a
47	chr8:60032794-60032844	PFSK-1	brain:	n/a
48	chr8:60032794-60032844	GM19239	blood:	n/a
49	chr8:60032794-60032844	SK-N-SH_RA	brain:	n/a
50	chr8:60032794-60032844	A549	lung:	n/a

No data

Variant related genes	Relation type
TOX	TF binding region
TOX	CpG island

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16924622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924642	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172654	1.00[YRI][hapmap]
rs2278957	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2956799	1.00[YRI][hapmap]
rs310369	1.00[YRI][hapmap]
rs61297458	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996132	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs866112	1.00[YRI][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	nsv831327	chr8:60008412-60159152	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3524312	chr8:60030498-60033446	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3524313	chr8:60030498-60033446	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3358496	chr8:60030823-60033771	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290526	LYN	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:60027600-60033200	Active TSS	Brain Angular Gyrus	brain
2	chr8:60027600-60033200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr8:60028000-60033000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr8:60028400-60033000	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr8:60028400-60033000	Active TSS	NH-A	brain
6	chr8:60029000-60033200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:60029200-60033000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr8:60029200-60033000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:60029200-60033200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr8:60029400-60033000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:60029600-60033000	Active TSS	Fetal Kidney	kidney
12	chr8:60029600-60033000	Active TSS	NHDF-Ad	bronchial
13	chr8:60029800-60033000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:60029800-60033000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:60029800-60033000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:60029800-60033000	Active TSS	Primary T cells from cord blood	blood
17	chr8:60029800-60033000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr8:60029800-60033000	Active TSS	Right Atrium	heart
19	chr8:60029800-60033000	Active TSS	HSMM	muscle
20	chr8:60030000-60033000	Active TSS	Osteobl	bone
21	chr8:60030200-60033200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr8:60030400-60033000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr8:60030400-60033000	Active TSS	Fetal Lung	lung
24	chr8:60030400-60033000	Active TSS	HSMMtube	muscle
25	chr8:60030400-60033200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr8:60030400-60033200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:60030400-60033400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr8:60030600-60033000	Active TSS	Brain Substantia Nigra	brain
29	chr8:60031000-60033000	Active TSS	Brain Germinal Matrix	brain
30	chr8:60031000-60033200	Active TSS	Fetal Stomach	stomach
31	chr8:60031600-60033000	Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr8:60031600-60033000	Active TSS	Brain Cingulate Gyrus	brain
33	chr8:60031600-60033200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
34	chr8:60031600-60033400	Active TSS	Stomach Smooth Muscle	stomach
35	chr8:60032200-60033000	Flanking Active TSS	Liver	Liver
36	chr8:60032400-60033000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr8:60032400-60033000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr8:60032400-60033000	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr8:60032400-60033000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr8:60032400-60033000	Flanking Active TSS	Right Ventricle	heart
41	chr8:60032400-60033200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr8:60032400-60033400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr8:60032400-60033400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr8:60032400-60033400	Transcr. at gene 5' and 3'	Dnd41	blood
45	chr8:60032600-60033000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr8:60032600-60033000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr8:60032600-60033000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr8:60032600-60033000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:60032600-60033000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr8:60032600-60033000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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