Variant report

Variant	rs4744171
Chromosome Location	chr9:95860415-95860416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr9:95858921-95860509	HEK293-T-REx	kidney:	n/a	chr9:95859281-95859290
2	SMARCB1	chr9:95860161-95861202	Hela-S3	cervix:	n/a	chr9:95861045-95861054
3	MXI1	chr9:95859931-95861394	IMR90	lung:	n/a	n/a
4	RCOR1	chr9:95860188-95862102	IMR90	lung:	n/a	n/a
5	HMGN3	chr9:95860233-95860429	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
2	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:
3	chr9:95857571..95862229-chr9:96211597..96216359,5	K562	blood:
4	chr9:95810158..95812137-chr9:95860234..95862505,2	K562	blood:
5	chr9:95816364..95826268-chr9:95852309..95863275,20	MCF-7	breast:
6	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
7	chr9:95855552..95862102-chr9:95867626..95876894,17	K562	blood:
8	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223446	TF binding region
ENSG00000157303	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10739942	0.96[ASN][1000 genomes]
rs10761193	0.96[ASN][1000 genomes]
rs10821067	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821069	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10821070	0.85[ASN][1000 genomes]
rs10821071	0.95[ASN][1000 genomes]
rs1123000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539672	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2027585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2298242	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819011	0.98[ASN][1000 genomes]
rs4077822	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237219	0.99[ASN][1000 genomes]
rs4333675	0.98[ASN][1000 genomes]
rs4384040	0.97[ASN][1000 genomes]
rs4743882	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743883	1.00[ASN][1000 genomes]
rs4743884	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4743885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4743887	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4744172	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744174	0.99[ASN][1000 genomes]
rs4744175	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4744176	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020130	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857595	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	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4744171	C9orf89	cis	Esophagus Mucosa	GTEx
rs4744171	C9orf89	cis	parietal	SCAN
rs4744171	C9orf89	cis	cerebellum	SCAN
rs4744171	C9orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95858600-95861000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:95858600-95861000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:95858800-95861000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr9:95858800-95861000	Flanking Active TSS	Colonic Mucosa	Colon
5	chr9:95858800-95861200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr9:95858800-95861200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr9:95858800-95861800	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr9:95859000-95861000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr9:95859000-95861000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr9:95859000-95861000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr9:95859000-95861000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr9:95859000-95861000	Flanking Active TSS	Hela-S3	cervix
13	chr9:95859000-95861000	Flanking Active TSS	HSMMtube	muscle
14	chr9:95859000-95861000	Flanking Active TSS	HUVEC	blood vessel
15	chr9:95859000-95861000	Flanking Active TSS	NHEK	skin
16	chr9:95859000-95861200	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr9:95859000-95861200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr9:95859000-95861200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr9:95859000-95861200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr9:95859000-95861200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:95859000-95861200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr9:95859000-95861400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:95859000-95861800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr9:95859000-95862000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:95859000-95862800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:95859200-95861000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:95859200-95861000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:95859200-95861000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr9:95859200-95861000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr9:95859200-95861000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr9:95859200-95861000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:95859200-95861000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr9:95859200-95861000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:95859200-95861000	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr9:95859200-95861000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr9:95859200-95861000	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr9:95859200-95861000	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr9:95859200-95861000	Flanking Active TSS	HMEC	breast
40	chr9:95859200-95861000	Flanking Active TSS	HSMM	muscle
41	chr9:95859200-95861000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr9:95859200-95861000	Flanking Active TSS	Osteobl	bone
43	chr9:95859200-95861200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:95859200-95861200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr9:95859200-95861200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:95859200-95861200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:95859200-95861200	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr9:95859200-95861200	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr9:95859200-95861200	Flanking Active TSS	A549	lung
50	chr9:95859200-95861200	Flanking Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links