Variant report

Variant	rs12337498
Chromosome Location	chr9:116031640-116031641
allele	C/T
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	chr9:116027249..116028822-chr9:116029570..116032042,2	MCF-7	breast:
3	chr9:115911868..115913830-chr9:116031326..116033544,3	K562	blood:
4	chr9:116031284..116035003-chr9:116035037..116039754,9	K562	blood:

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

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10116039	0.86[CEU][hapmap]
rs10120404	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10123780	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]
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];0.82[JPT][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]
rs12337709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342489	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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][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];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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12337498	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs12337498	CDC26	cis	Heart Left Ventricle	GTEx
rs12337498	CDC26	cis	Thyroid	GTEx
rs12337498	PRPF4	cis	Stomach	GTEx
rs12337498	PRPF4	cis	lung	GTEx
rs12337498	CDC26	cis	Muscle Skeletal	GTEx
rs12337498	PRPF4	cis	Thyroid	GTEx

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	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
3	chr9:116017600-116031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
7	chr9:116021200-116032200	Weak transcription	Small Intestine	intestine
8	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:116021400-116032200	Weak transcription	Pancreas	Pancrea
10	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
11	chr9:116022800-116031800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:116022800-116032200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:116022800-116032200	Weak transcription	Esophagus	oesophagus
14	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:116023000-116031800	Weak transcription	NHLF	lung
16	chr9:116023000-116032200	Weak transcription	Gastric	stomach
17	chr9:116023000-116033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:116023000-116033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:116023200-116031800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:116023200-116031800	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:116023400-116032200	Weak transcription	Right Ventricle	heart
23	chr9:116023400-116034200	Weak transcription	Colonic Mucosa	Colon
24	chr9:116023600-116032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:116024800-116031800	Weak transcription	HSMMtube	muscle
26	chr9:116024800-116032200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:116024800-116032200	Weak transcription	Lung	lung
28	chr9:116025200-116031800	Weak transcription	HMEC	breast
29	chr9:116026600-116035800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:116026800-116036000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:116027000-116035800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:116027000-116035800	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:116027200-116032200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:116027200-116033600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:116027200-116035200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:116027200-116035800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:116027200-116036000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr9:116027200-116036000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr9:116027200-116036200	Strong transcription	Primary T cells from cord blood	blood
40	chr9:116027400-116036000	Strong transcription	Fetal Muscle Leg	muscle
41	chr9:116027800-116036200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:116028000-116032200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:116028000-116036000	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr9:116028200-116035800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116028400-116031800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr9:116028400-116035400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr9:116028400-116036000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr9:116028400-116036000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:116028400-116036200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:116028600-116031800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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