Variant report

Variant	rs17593496
Chromosome Location	chr9:95872885-95872886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
2	chr9:95870068..95872705-chr9:95872843..95876016,3	MCF-7	breast:
3	chr9:95856250..95859109-chr9:95872674..95874497,2	MCF-7	breast:
4	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
5	chr9:95872784..95874887-chr9:95916716..95918233,2	K562	blood:
6	chr9:95870960..95873239-chr9:95894940..95897821,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12003264	0.88[GIH][hapmap]
rs13284731	0.87[GIH][hapmap]
rs13285107	0.87[GIH][hapmap]
rs13286624	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs13288200	0.88[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs62573571	1.00[AFR][1000 genomes]
rs7025686	0.87[YRI][hapmap]
rs72741081	0.92[AMR][1000 genomes];0.99[EUR][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	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17593496	C9orf89	cis	multi-tissue	Pritchard
rs17593496	NINJ1	cis	uninvolved skin	skin_eQTL
rs17593496	NINJ1	cis	brain	seeQTL
rs17593496	NINJ1	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95859400-95876200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
3	chr9:95860400-95876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:95861800-95882000	Weak transcription	HSMMtube	muscle
5	chr9:95862000-95873800	Weak transcription	NH-A	brain
6	chr9:95862000-95878400	Weak transcription	Stomach Mucosa	stomach
7	chr9:95862000-95881800	Weak transcription	HUVEC	blood vessel
8	chr9:95862200-95878000	Weak transcription	HSMM	muscle
9	chr9:95862200-95878600	Weak transcription	Psoas Muscle	Psoas
10	chr9:95862200-95878600	Weak transcription	Right Atrium	heart
11	chr9:95862400-95873000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:95866600-95878600	Weak transcription	NHDF-Ad	bronchial
13	chr9:95867000-95878400	Weak transcription	Fetal Lung	lung
14	chr9:95867800-95873400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:95869000-95877600	Strong transcription	Fetal Intestine Small	intestine
16	chr9:95869200-95877600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:95869400-95877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:95869400-95877400	Strong transcription	NHLF	lung
19	chr9:95869600-95876400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:95869600-95877400	Strong transcription	Fetal Stomach	stomach
21	chr9:95869800-95876000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr9:95869800-95876400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr9:95869800-95876800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr9:95869800-95877400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:95869800-95877400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:95870000-95876600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:95870200-95876400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:95870200-95877400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:95870400-95873000	Weak transcription	Left Ventricle	heart
31	chr9:95870600-95873600	Strong transcription	NHEK	skin
32	chr9:95870600-95875000	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr9:95870800-95873800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr9:95871000-95894200	Weak transcription	Dnd41	blood
35	chr9:95871200-95874400	Weak transcription	A549	lung
36	chr9:95871200-95874800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:95871200-95878400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:95871200-95878400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:95871200-95878400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:95871400-95873000	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:95871400-95873600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:95871600-95873000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:95871600-95876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr9:95871600-95877200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr9:95871600-95882000	Weak transcription	GM12878-XiMat	blood
46	chr9:95871800-95873400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:95871800-95873600	Strong transcription	Brain Angular Gyrus	brain
48	chr9:95871800-95876200	Strong transcription	Fetal Muscle Leg	muscle
49	chr9:95871800-95876600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr9:95871800-95876600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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