Variant report

Variant	rs2398827
Chromosome Location	chr9:95907107-95907108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95895264..95898192-chr9:95905640..95908548,4	MCF-7	breast:
2	chr9:95905509..95907695-chr9:96212278..96215177,2	MCF-7	breast:
3	chr9:95890205..95893165-chr9:95905253..95907697,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10761195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821075	0.80[CHB][hapmap]
rs10821076	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs10992653	0.97[ASN][1000 genomes]
rs1833035	0.98[ASN][1000 genomes]
rs2398825	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743896	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744181	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2398827	NINJ1	cis	cerebellum	SCAN
rs2398827	ROR2	cis	parietal	SCAN
rs2398827	NINJ1	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95899600-95907200	Enhancers	Fetal Thymus	thymus
2	chr9:95899800-95907400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr9:95899800-95922200	Weak transcription	Gastric	stomach
4	chr9:95901600-95907800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:95901800-95907400	Enhancers	Primary T cells from cord blood	blood
6	chr9:95902400-95907400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:95903000-95907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:95904000-95907200	Enhancers	Fetal Muscle Leg	muscle
9	chr9:95904200-95907200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr9:95904200-95907200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:95904400-95907200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:95904800-95911600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:95905200-95907800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr9:95905400-95907200	Enhancers	Pancreas	Pancrea
15	chr9:95905600-95907200	Enhancers	HMEC	breast
16	chr9:95905600-95907400	Enhancers	Primary hematopoietic stem cells	blood
17	chr9:95905600-95907400	Enhancers	Dnd41	blood
18	chr9:95905600-95907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:95906200-95907200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:95906200-95907200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr9:95906200-95907200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:95906200-95907200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:95906200-95907200	Enhancers	Brain Angular Gyrus	brain
24	chr9:95906200-95907200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr9:95906200-95907200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:95906200-95907200	Enhancers	Esophagus	oesophagus
27	chr9:95906200-95907200	Enhancers	Fetal Brain Male	brain
28	chr9:95906200-95907200	Enhancers	Fetal Heart	heart
29	chr9:95906200-95907200	Enhancers	Placenta	Placenta
30	chr9:95906200-95907200	Enhancers	Psoas Muscle	Psoas
31	chr9:95906200-95907200	Enhancers	Right Atrium	heart
32	chr9:95906200-95907200	Enhancers	Right Ventricle	heart
33	chr9:95906200-95907200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr9:95906200-95907200	Enhancers	Stomach Smooth Muscle	stomach
35	chr9:95906200-95907200	Enhancers	Hela-S3	cervix
36	chr9:95906200-95907200	Enhancers	NHEK	skin
37	chr9:95906200-95907400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr9:95906200-95907400	Enhancers	Brain Substantia Nigra	brain
39	chr9:95906400-95907200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr9:95906400-95907200	Enhancers	HSMM	muscle
41	chr9:95906600-95907200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr9:95906600-95907200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:95906600-95907200	Enhancers	HepG2	liver
44	chr9:95906600-95907400	Enhancers	Brain Germinal Matrix	brain
45	chr9:95906600-95907600	Enhancers	Primary T cells fromperipheralblood	blood
46	chr9:95906800-95907200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:95906800-95907400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:95906800-95907400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr9:95906800-95907600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr9:95906800-95910000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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