Variant report

Variant	rs12235416
Chromosome Location	chr9:95888667-95888668
allele	C/T
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	POLR2A	chr9:95888517-95888918	GM12878	blood:	n/a	n/a
2	ELF1	chr9:95888353-95888880	GM12878	blood:	n/a	n/a
3	POLR2A	chr9:95888633-95889725	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95857275..95859572-chr9:95888374..95892185,3	MCF-7	breast:
2	chr9:95856977..95859126-chr9:95888088..95890598,2	MCF-7	breast:

Variant related genes	Relation type
NINJ1	TF binding region
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10992645	0.97[ASN][1000 genomes]
rs12237655	0.97[ASN][1000 genomes]
rs12238760	0.96[ASN][1000 genomes]
rs13284731	0.81[TSI][hapmap]
rs13285107	0.81[TSI][hapmap]
rs13298119	0.87[TSI][hapmap]
rs60629714	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7018885	0.82[ASN][1000 genomes]
rs7032525	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7033638	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618189	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv614879	chr9:95883363-95897564	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12235416	NINJ1	cis	Thyroid	GTEx
rs12235416	NOL8	cis	cerebellum	SCAN
rs12235416	NINJ1	cis	cerebellum	SCAN
rs12235416	NINJ1	cis	multi-tissue	Pritchard
rs12235416	NINJ1	cis	Esophagus Muscularis	GTEx
rs12235416	NINJ1	cis	uninvolved skin	skin_eQTL
rs12235416	NINJ1	cis	Artery Tibial	GTEx
rs12235416	NINJ1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
2	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:95871000-95894200	Weak transcription	Dnd41	blood
4	chr9:95873400-95888800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:95877000-95889200	Weak transcription	Fetal Brain Female	brain
6	chr9:95877200-95888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:95879200-95889000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:95882800-95889000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:95882800-95889200	Weak transcription	HSMM	muscle
10	chr9:95882800-95889200	Weak transcription	NH-A	brain
11	chr9:95883000-95889000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:95883000-95894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:95883000-95895000	Weak transcription	HSMMtube	muscle
14	chr9:95883000-95895000	Weak transcription	K562	blood
15	chr9:95883200-95888800	Weak transcription	Psoas Muscle	Psoas
16	chr9:95883600-95888800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:95883600-95888800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr9:95883800-95888800	Strong transcription	Aorta	Aorta
19	chr9:95884200-95889200	Strong transcription	Gastric	stomach
20	chr9:95885000-95895400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:95885200-95888800	Weak transcription	Primary B cells from cord blood	blood
22	chr9:95886000-95890600	Enhancers	Fetal Thymus	thymus
23	chr9:95886200-95888800	Weak transcription	Fetal Brain Male	brain
24	chr9:95886200-95889000	Genic enhancers	Spleen	Spleen
25	chr9:95886400-95888800	Weak transcription	Fetal Heart	heart
26	chr9:95886600-95889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:95886600-95889400	Weak transcription	GM12878-XiMat	blood
28	chr9:95886800-95888800	Weak transcription	HMEC	breast
29	chr9:95886800-95895400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:95887200-95888800	Genic enhancers	Rectal Mucosa Donor 29	rectum
31	chr9:95887200-95891200	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr9:95887400-95890400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:95887400-95890800	Weak transcription	A549	lung
34	chr9:95887400-95891600	Weak transcription	Ovary	ovary
35	chr9:95887400-95893600	Weak transcription	NHLF	lung
36	chr9:95887600-95888800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr9:95887600-95889000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:95887600-95889200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:95887600-95890800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr9:95887600-95894800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr9:95887800-95888800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr9:95887800-95889000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:95887800-95889000	Weak transcription	Stomach Mucosa	stomach
44	chr9:95887800-95893400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr9:95887800-95894000	Weak transcription	Brain Germinal Matrix	brain
46	chr9:95888000-95888800	Genic enhancers	Colon Smooth Muscle	Colon
47	chr9:95888000-95888800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:95888000-95889000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:95888000-95889000	Genic enhancers	Placenta	Placenta
50	chr9:95888000-95890400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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