Variant report

Variant	rs12350705
Chromosome Location	chr9:116027484-116027485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116023106..116028620-chr9:116032404..116039334,10	MCF-7	breast:
2	chr9:116025697..116028856-chr9:116035797..116038156,5	K562	blood:
3	chr9:116025855..116027571-chr9:116035430..116037680,2	MCF-7	breast:
4	chr9:116011649..116014033-chr9:116026530..116028582,2	K562	blood:
5	chr9:116027249..116028822-chr9:116029570..116032042,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176386	Chromatin interaction
ENSG00000136875	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10120404	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10123780	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10125030	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10981723	0.88[EUR][1000 genomes]
rs11789775	0.89[EUR][1000 genomes]
rs11794214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11794663	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12337498	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12337709	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17763934	0.89[EUR][1000 genomes]
rs17764013	0.89[EUR][1000 genomes]
rs17831500	0.89[EUR][1000 genomes]
rs3087548	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3810918	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3810919	0.95[EUR][1000 genomes]
rs4979229	0.95[EUR][1000 genomes];0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12350705	CDC26	cis	Thyroid	GTEx
rs12350705	PRPF4	cis	Thyroid	GTEx
rs12350705	CDC26	cis	Muscle Skeletal	GTEx
rs12350705	CDC26	cis	Heart Left Ventricle	GTEx
rs12350705	PRPF4	cis	lung	GTEx
rs12350705	PRPF4	cis	Stomach	GTEx
rs12350705	CDC26	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:116009600-116029800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
5	chr9:116011400-116028800	Weak transcription	Fetal Kidney	kidney
6	chr9:116017600-116031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:116018000-116027600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:116019200-116028800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:116020000-116029600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:116020600-116031600	Weak transcription	HUVEC	blood vessel
13	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
14	chr9:116021200-116031600	Weak transcription	Fetal Brain Male	brain
15	chr9:116021200-116032200	Weak transcription	Small Intestine	intestine
16	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:116021400-116029800	Weak transcription	Primary B cells from cord blood	blood
18	chr9:116021400-116032200	Weak transcription	Pancreas	Pancrea
19	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
20	chr9:116022600-116028600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr9:116022600-116029400	Weak transcription	NH-A	brain
22	chr9:116022600-116031600	Weak transcription	NHDF-Ad	bronchial
23	chr9:116022800-116028600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:116022800-116028600	Weak transcription	Fetal Thymus	thymus
25	chr9:116022800-116029000	Weak transcription	A549	lung
26	chr9:116022800-116030200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:116022800-116030600	Weak transcription	K562	blood
28	chr9:116022800-116031600	Weak transcription	Psoas Muscle	Psoas
29	chr9:116022800-116031800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:116022800-116032200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:116022800-116032200	Weak transcription	Esophagus	oesophagus
32	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:116023000-116028400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr9:116023000-116028600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr9:116023000-116028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:116023000-116029800	Weak transcription	Thymus	Thymus
37	chr9:116023000-116029800	Weak transcription	Spleen	Spleen
38	chr9:116023000-116031400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr9:116023000-116031800	Weak transcription	NHLF	lung
40	chr9:116023000-116032200	Weak transcription	Gastric	stomach
41	chr9:116023000-116033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:116023000-116033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:116023200-116027800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr9:116023200-116028400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:116023200-116031600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:116023200-116031800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr9:116023200-116031800	Weak transcription	Colon Smooth Muscle	Colon
49	chr9:116023400-116030200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:116023400-116032200	Weak transcription	Right Ventricle	heart

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