Variant report

Variant	rs763920
Chromosome Location	chr17:67090200-67090201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:67043107..67046503-chr17:67087487..67090701,3	K562	blood:
2	chr17:67083309..67086380-chr17:67087124..67091050,4	K562	blood:
3	chr17:67088137..67090811-chr17:67098460..67099975,2	K562	blood:
4	chr17:67083309..67086941-chr17:67087664..67091050,5	K562	blood:
5	chr17:67087494..67092191-chr17:67094325..67097858,5	K562	blood:
6	chr17:67088212..67090645-chr17:67172453..67175365,2	K562	blood:

Variant related genes	Relation type
ENSG00000154262	Chromatin interaction
ENSG00000154258	Chromatin interaction
ENSG00000265331	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11077942	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652530	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs11654867	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11657954	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659091	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs12453921	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939282	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs12942011	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12942993	0.98[ASN][1000 genomes]
rs1974575	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2041171	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs2098034	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302132	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302133	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302134	0.88[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2302290	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364315	0.95[CEU][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3744489	0.83[TSI][hapmap]
rs4141177	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs4968833	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968995	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740517	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9282552	0.85[EUR][1000 genomes]
rs9914684	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1066998	chr17:67060038-67090475	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv908705	chr17:67061898-67112456	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	esv1850212	chr17:67081732-67117428	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs763920	CD79B	cis	cerebellum	SCAN
rs763920	ABCA9	cis	parietal	SCAN
rs763920	CACNG5	cis	cerebellum	SCAN
rs763920	ABCA6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67067200-67099600	Weak transcription	Gastric	stomach
2	chr17:67067200-67111600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:67071800-67091400	Weak transcription	Brain Anterior Caudate	brain
4	chr17:67076800-67109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr17:67079400-67090600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr17:67079400-67093600	Weak transcription	Fetal Stomach	stomach
8	chr17:67079400-67095600	Weak transcription	Psoas Muscle	Psoas
9	chr17:67079400-67112200	Strong transcription	Liver	Liver
10	chr17:67079400-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr17:67079400-67117600	Weak transcription	Esophagus	oesophagus
12	chr17:67079600-67091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:67079600-67101200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:67079600-67114200	Weak transcription	NHDF-Ad	bronchial
15	chr17:67080800-67090800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr17:67080800-67112000	Weak transcription	Brain Substantia Nigra	brain
17	chr17:67081200-67090800	Weak transcription	Fetal Muscle Leg	muscle
18	chr17:67081200-67102000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr17:67081400-67090400	Weak transcription	Left Ventricle	heart
20	chr17:67081400-67095000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr17:67081400-67118600	Weak transcription	Right Ventricle	heart
22	chr17:67082200-67114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr17:67083800-67090200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr17:67085800-67099600	Weak transcription	Lung	lung
25	chr17:67087000-67114600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:67087000-67130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:67088400-67090600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr17:67088800-67090400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:67089000-67090200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:67089600-67091200	Enhancers	HepG2	liver
31	chr17:67089600-67093400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:67089600-67097200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr17:67089800-67090200	Flanking Active TSS	K562	blood
34	chr17:67089800-67090400	Enhancers	Primary B cells from cord blood	blood
35	chr17:67089800-67090400	Weak transcription	Adipose Nuclei	Adipose
36	chr17:67089800-67090600	Enhancers	Primary hematopoietic stem cells	blood
37	chr17:67089800-67090600	Weak transcription	Ovary	ovary
38	chr17:67089800-67090800	Weak transcription	Thymus	Thymus
39	chr17:67089800-67091200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:67089800-67093600	Weak transcription	Primary T cells from cord blood	blood
41	chr17:67089800-67095800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:67089800-67102200	Weak transcription	GM12878-XiMat	blood
43	chr17:67090000-67090400	Weak transcription	Fetal Kidney	kidney
44	chr17:67090000-67091000	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr17:67090000-67092200	Strong transcription	Fetal Lung	lung
46	chr17:67090200-67090600	Enhancers	Stomach Mucosa	stomach
47	chr17:67090200-67091400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:67090200-67092200	Enhancers	K562	blood
49	chr17:67090200-67094400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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