Variant report

Variant	rs4968898
Chromosome Location	chr17:66505856-66505857
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr17:66505676-66506305	ECC-1	luminal epithelium:	n/a	n/a
2	KAP1	chr17:66505782-66506962	U2OS	brain:	n/a	n/a
3	MYBL2	chr17:66505332-66506150	HepG2	liver:	n/a	n/a
4	EP300	chr17:66505649-66506085	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:66505803-66506169	HepG2	liver:	n/a	n/a
6	ARID3A	chr17:66505607-66506034	HepG2	liver:	n/a	n/a
7	ELF1	chr17:66505811-66506202	HepG2	liver:	n/a	chr17:66505993-66506006
8	ELF1	chr17:66505855-66506126	K562	blood:	n/a	chr17:66505993-66506006
9	FOXA1	chr17:66504998-66505907	HepG2	liver:	n/a	n/a
10	KAP1	chr17:66505726-66506990	HEK293	kidney:	n/a	n/a
11	SPI1	chr17:66505715-66506290	HL-60	blood:	n/a	chr17:66506227-66506240
12	MYBL2	chr17:66505402-66506200	HepG2	liver:	n/a	n/a
13	NFIC	chr17:66505713-66506309	ECC-1	luminal epithelium:	n/a	n/a
14	YY1	chr17:66505811-66506167	HepG2	liver:	n/a	n/a
15	MXI1	chr17:66505816-66506181	HepG2	liver:	n/a	n/a
16	HEY1	chr17:66505225-66506330	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66242526..66245524-chr17:66505598..66508247,2	MCF-7	breast:
2	chr17:66503157..66506597-chr17:66507024..66509568,3	K562	blood:

Variant related genes	Relation type
PRKAR1A	TF binding region
ENSG00000108946	Chromatin interaction
ENSG00000265100	Chromatin interaction
ENSG00000196704	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs16972990	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286561	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs2286562	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap]
rs2952279	0.86[GIH][hapmap];0.91[MEX][hapmap]
rs2952280	0.86[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs72845684	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72845685	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72847770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847779	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8079916	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4968898	CD79B	cis	cerebellum	SCAN
rs4968898	PRKAR1A	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66502000-66507600	Weak transcription	Left Ventricle	heart
2	chr17:66503400-66506200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:66503600-66507400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:66503600-66507400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr17:66503600-66507600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr17:66504000-66507400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:66504200-66506000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:66504200-66507200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:66504200-66507400	Weak transcription	NHLF	lung
10	chr17:66504200-66507400	Weak transcription	Osteobl	bone
11	chr17:66504200-66507600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:66504400-66506000	Weak transcription	Liver	Liver
13	chr17:66504400-66507000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:66504400-66507600	Weak transcription	HSMMtube	muscle
15	chr17:66505000-66506800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr17:66505000-66507400	Enhancers	Primary B cells from cord blood	blood
17	chr17:66505000-66507400	Enhancers	Adipose Nuclei	Adipose
18	chr17:66505200-66506000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:66505200-66506200	Enhancers	Fetal Muscle Trunk	muscle
20	chr17:66505200-66506800	Weak transcription	Brain Angular Gyrus	brain
21	chr17:66505200-66507200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr17:66505200-66507200	Flanking Active TSS	HepG2	liver
23	chr17:66505200-66507400	Enhancers	Fetal Lung	lung
24	chr17:66505200-66507400	Enhancers	Fetal Muscle Leg	muscle
25	chr17:66505200-66507400	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr17:66505200-66507600	Enhancers	HUVEC	blood vessel
27	chr17:66505400-66506000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr17:66505400-66506000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr17:66505400-66506400	Enhancers	Fetal Heart	heart
30	chr17:66505400-66507200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:66505400-66507600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr17:66505400-66507600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:66505400-66507600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:66505600-66506400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr17:66505600-66506600	Weak transcription	Psoas Muscle	Psoas
36	chr17:66505600-66506600	Enhancers	HSMM	muscle
37	chr17:66505600-66507200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:66505600-66507200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:66505600-66507200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:66505600-66507200	Enhancers	GM12878-XiMat	blood
41	chr17:66505600-66507400	Enhancers	Primary hematopoietic stem cells	blood
42	chr17:66505800-66506000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:66505800-66506000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr17:66505800-66506200	Enhancers	Colonic Mucosa	Colon
45	chr17:66505800-66506200	Enhancers	Duodenum Mucosa	Duodenum
46	chr17:66505800-66506200	Enhancers	Fetal Thymus	thymus
47	chr17:66505800-66506600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:66505800-66506600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:66505800-66506600	Enhancers	HMEC	breast
50	chr17:66505800-66506600	Enhancers	NHEK	skin

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