Variant report

Variant	rs56145587
Chromosome Location	chr9:95875381-95875382
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95870682..95872423-chr9:95874174..95876146,2	K562	blood:
2	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
3	chr9:95870068..95872705-chr9:95872843..95876016,3	MCF-7	breast:
4	chr9:95874739..95878921-chr9:95879079..95884047,10	K562	blood:
5	chr9:95874371..95880149-chr9:95880216..95885255,14	K562	blood:
6	chr9:95869643..95873929-chr9:95874567..95878954,6	MCF-7	breast:
7	chr9:95856601..95858475-chr9:95874863..95877124,2	K562	blood:

Variant related genes	Relation type
ENSG00000223446	Chromatin interaction
ENSG00000165233	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11789113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790871	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55900494	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56164749	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59780701	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741072	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741078	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56145587	C9orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 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	chr9:95862000-95878400	Weak transcription	Stomach Mucosa	stomach
6	chr9:95862000-95881800	Weak transcription	HUVEC	blood vessel
7	chr9:95862200-95878000	Weak transcription	HSMM	muscle
8	chr9:95862200-95878600	Weak transcription	Psoas Muscle	Psoas
9	chr9:95862200-95878600	Weak transcription	Right Atrium	heart
10	chr9:95866600-95878600	Weak transcription	NHDF-Ad	bronchial
11	chr9:95867000-95878400	Weak transcription	Fetal Lung	lung
12	chr9:95869000-95877600	Strong transcription	Fetal Intestine Small	intestine
13	chr9:95869200-95877600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr9:95869400-95877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:95869400-95877400	Strong transcription	NHLF	lung
16	chr9:95869600-95876400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:95869600-95877400	Strong transcription	Fetal Stomach	stomach
18	chr9:95869800-95876000	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr9:95869800-95876400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr9:95869800-95876800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr9:95869800-95877400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:95869800-95877400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:95870000-95876600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:95870200-95876400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:95870200-95877400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:95871000-95894200	Weak transcription	Dnd41	blood
28	chr9:95871200-95878400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:95871200-95878400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:95871200-95878400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:95871600-95876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:95871600-95877200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:95871600-95882000	Weak transcription	GM12878-XiMat	blood
34	chr9:95871800-95876200	Strong transcription	Fetal Muscle Leg	muscle
35	chr9:95871800-95876600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr9:95871800-95876600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:95871800-95876800	Strong transcription	Colon Smooth Muscle	Colon
38	chr9:95872000-95876600	Strong transcription	Brain Cingulate Gyrus	brain
39	chr9:95872200-95875400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr9:95872200-95876200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:95872200-95876400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:95872200-95876600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr9:95872200-95877200	Weak transcription	Hela-S3	cervix
44	chr9:95872200-95881600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr9:95872200-95882000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:95872400-95875400	Genic enhancers	Spleen	Spleen
47	chr9:95872400-95876000	Strong transcription	Brain Substantia Nigra	brain
48	chr9:95872400-95876600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:95872400-95876600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:95872400-95876600	Strong transcription	Fetal Intestine Large	intestine

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