Variant report

Variant	rs10123780
Chromosome Location	chr9:116032383-116032384
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116024711..116027399-chr9:116031082..116034074,3	MCF-7	breast:
2	chr9:115911868..115913830-chr9:116031326..116033544,3	K562	blood:
3	chr9:116031284..116035003-chr9:116035037..116039754,9	K562	blood:

Variant related genes	Relation type
ENSG00000136867	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10116039	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs10120404	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125030	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125032	0.90[AFR][1000 genomes]
rs10513190	1.00[CHB][hapmap]
rs10817474	0.86[CEU][hapmap]
rs10981723	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs11789775	0.92[EUR][1000 genomes]
rs11793978	1.00[CHB][hapmap]
rs11794214	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11794663	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12337498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342489	0.91[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs12350705	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16931988	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs17763351	1.00[CHB][hapmap]
rs17763934	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17764013	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17831500	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2233913	1.00[CHB][hapmap]
rs3087548	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088235	0.86[CEU][hapmap]
rs3810917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3810918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810919	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs41307479	0.81[EUR][1000 genomes]
rs4979229	0.98[EUR][1000 genomes];1.00[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10123780	PRPF4	cis	lung	GTEx
rs10123780	CDC26	cis	parietal	SCAN
rs10123780	CDC26	cis	Muscle Skeletal	GTEx
rs10123780	CDC26	cis	cerebellum	SCAN
rs10123780	PRPF4	cis	Stomach	GTEx
rs10123780	CDC26	cis	Thyroid	GTEx
rs10123780	CDC26	cis	Heart Left Ventricle	GTEx
rs10123780	PRPF4	cis	Thyroid	GTEx
rs10123780	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs10123780	HDHD3	cis	lymphoblastoid	seeQTL
rs10123780	ZNF483	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
5	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
7	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:116023000-116033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:116023000-116033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:116023400-116034200	Weak transcription	Colonic Mucosa	Colon
12	chr9:116026600-116035800	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:116026800-116036000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:116027000-116035800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:116027000-116035800	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:116027200-116033600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:116027200-116035200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:116027200-116035800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:116027200-116036000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:116027200-116036000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr9:116027200-116036200	Strong transcription	Primary T cells from cord blood	blood
22	chr9:116027400-116036000	Strong transcription	Fetal Muscle Leg	muscle
23	chr9:116027800-116036200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:116028000-116036000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:116028200-116035800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:116028400-116035400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:116028400-116036000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr9:116028400-116036000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr9:116028400-116036200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:116028600-116034400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr9:116028600-116035800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:116028600-116035800	Strong transcription	Adipose Nuclei	Adipose
33	chr9:116028600-116036000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:116028600-116036000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:116028600-116036000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr9:116028600-116036000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:116028600-116036000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:116028600-116036000	Strong transcription	Placenta	Placenta
39	chr9:116028800-116035400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:116028800-116035600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:116028800-116035800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:116028800-116035800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:116028800-116035800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:116028800-116035800	Strong transcription	Dnd41	blood
45	chr9:116029000-116034200	Strong transcription	HSMM	muscle
46	chr9:116029000-116035400	Strong transcription	A549	lung
47	chr9:116029000-116035600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:116029000-116035800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:116029000-116036000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:116029000-116036000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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