Variant report

Variant	rs6478004
Chromosome Location	chr9:116108669-116108670
allele	A/G
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	EP300	chr9:116108550-116109342	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116106104..116109704-chr9:116111339..116114258,3	K562	blood:
2	chr9:116038056..116040048-chr9:116108621..116111534,2	MCF-7	breast:

Variant related genes	Relation type
BSPRY	TF binding region
ENSG00000119411	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10114327	0.88[ASN][1000 genomes]
rs10117906	0.84[ASN][1000 genomes]
rs10118045	0.84[ASN][1000 genomes]
rs10118275	0.86[ASN][1000 genomes]
rs10759640	0.90[ASN][1000 genomes]
rs10817481	0.88[ASN][1000 genomes]
rs10817485	0.84[ASN][1000 genomes]
rs10981734	0.81[ASN][1000 genomes]
rs10981762	0.84[ASN][1000 genomes]
rs10981763	0.84[ASN][1000 genomes]
rs10981764	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11787602	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16932730	0.81[ASN][1000 genomes]
rs1998504	0.88[ASN][1000 genomes]
rs2093691	0.90[ASN][1000 genomes]
rs2296075	0.82[ASN][1000 genomes]
rs4979237	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4979238	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478002	0.88[ASN][1000 genomes]
rs6478003	0.89[ASN][1000 genomes]
rs6478005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478006	0.85[ASN][1000 genomes]
rs7025188	0.84[ASN][1000 genomes]
rs7025333	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7025371	0.85[ASN][1000 genomes]
rs7025517	0.82[ASN][1000 genomes]
rs7025770	0.85[ASN][1000 genomes]
rs7026076	0.84[ASN][1000 genomes]
rs7041572	0.87[ASN][1000 genomes]
rs7048039	0.88[ASN][1000 genomes]
rs7849513	0.87[ASN][1000 genomes]
rs7850002	0.91[ASN][1000 genomes]
rs7850003	0.83[ASN][1000 genomes]
rs7850264	0.86[ASN][1000 genomes]
rs7863921	0.90[ASN][1000 genomes]
rs7864788	0.87[ASN][1000 genomes]
rs7868271	0.89[ASN][1000 genomes]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6478004	HDHD3	cis	Artery Tibial	GTEx
rs6478004	CDC26	cis	Thyroid	GTEx
rs6478004	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs6478004	BSPRY	cis	Heart Left Ventricle	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116103000-116111800	Weak transcription	Lung	lung
2	chr9:116103200-116108800	Weak transcription	Placenta	Placenta
3	chr9:116103200-116110000	Weak transcription	Right Atrium	heart
4	chr9:116103200-116111400	Weak transcription	Stomach Mucosa	stomach
5	chr9:116103200-116111400	Weak transcription	GM12878-XiMat	blood
6	chr9:116105400-116108800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:116105800-116110200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr9:116105800-116111400	Enhancers	Fetal Intestine Small	intestine
9	chr9:116105800-116111400	Weak transcription	Right Ventricle	heart
10	chr9:116106200-116111400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:116106400-116108800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:116106400-116109200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:116106400-116110400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:116106600-116109400	Weak transcription	Colonic Mucosa	Colon
15	chr9:116106600-116110000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:116106600-116111400	Weak transcription	Liver	Liver
17	chr9:116106600-116111400	Weak transcription	Esophagus	oesophagus
18	chr9:116106600-116111400	Weak transcription	Pancreas	Pancrea
19	chr9:116106600-116111800	Weak transcription	K562	blood
20	chr9:116107200-116108800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:116107600-116111600	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:116107800-116110000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:116107800-116110000	Weak transcription	Small Intestine	intestine
24	chr9:116107800-116111200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:116108000-116110000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:116108000-116110000	Weak transcription	Fetal Heart	heart
27	chr9:116108000-116111400	Weak transcription	Brain Anterior Caudate	brain
28	chr9:116108000-116111600	Weak transcription	Brain Angular Gyrus	brain
29	chr9:116108000-116112000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:116108200-116109600	Weak transcription	Fetal Intestine Large	intestine
31	chr9:116108200-116109600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr9:116108200-116111200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:116108200-116112000	Weak transcription	Brain Substantia Nigra	brain
34	chr9:116108400-116108800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:116108600-116109800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:116108600-116111400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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