Variant report

Variant	rs4744176
Chromosome Location	chr9:95872216-95872217
allele	G/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	chr9:95870093..95872225-chr9:96214291..96216786,2	K562	blood:
3	chr9:95855712..95863110-chr9:95867626..95874665,14	K562	blood:
4	chr9:95855064..95861522-chr9:95867449..95872462,10	MCF-7	breast:
5	chr9:95870960..95873239-chr9:95894940..95897821,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10739942	0.96[ASN][1000 genomes]
rs10761193	0.96[ASN][1000 genomes]
rs10821067	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821069	0.87[EUR][1000 genomes]
rs10821070	0.85[ASN][1000 genomes]
rs10821071	0.97[ASN][1000 genomes]
rs1123000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539672	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2027585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2275849	0.82[LWK][hapmap]
rs2298242	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819011	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4077822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237219	0.98[ASN][1000 genomes]
rs4333675	0.97[ASN][1000 genomes]
rs4384040	0.96[ASN][1000 genomes]
rs4743882	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743883	0.98[ASN][1000 genomes]
rs4743884	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4743885	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4743887	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4744171	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]
rs4744172	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744174	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4744175	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7020130	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7028778	0.81[AFR][1000 genomes]
rs7857595	0.98[ASN][1000 genomes]
rs7868952	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4744176	C9orf89	cis	Liver	GTEx
rs4744176	C9orf89	cis	parietal	SCAN
rs4744176	C9orf89	Cis_1M	lymphoblastoid	RTeQTL
rs4744176	C9orf89	cis	Esophagus Mucosa	GTEx
rs4744176	C9orf89	cis	lymphoblastoid	seeQTL
rs4744176	XM_210945	trans	multi-tissue	Pritchard
rs4744176	C9orf89	cis	multi-tissue	Pritchard
rs4744176	C9orf89	cis	cerebellum	SCAN

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	chr9:95860200-95872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:95860400-95876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:95860800-95872800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:95861800-95882000	Weak transcription	HSMMtube	muscle
7	chr9:95862000-95872800	Weak transcription	Osteobl	bone
8	chr9:95862000-95873800	Weak transcription	NH-A	brain
9	chr9:95862000-95878400	Weak transcription	Stomach Mucosa	stomach
10	chr9:95862000-95881800	Weak transcription	HUVEC	blood vessel
11	chr9:95862200-95878000	Weak transcription	HSMM	muscle
12	chr9:95862200-95878600	Weak transcription	Psoas Muscle	Psoas
13	chr9:95862200-95878600	Weak transcription	Right Atrium	heart
14	chr9:95862400-95873000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:95866600-95878600	Weak transcription	NHDF-Ad	bronchial
16	chr9:95867000-95878400	Weak transcription	Fetal Lung	lung
17	chr9:95867800-95872800	Weak transcription	Brain Germinal Matrix	brain
18	chr9:95867800-95873400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:95868400-95872600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:95869000-95877600	Strong transcription	Fetal Intestine Small	intestine
21	chr9:95869200-95877600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr9:95869400-95877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:95869400-95877400	Strong transcription	NHLF	lung
24	chr9:95869600-95872600	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr9:95869600-95876400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:95869600-95877400	Strong transcription	Fetal Stomach	stomach
27	chr9:95869800-95876000	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr9:95869800-95876400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr9:95869800-95876800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr9:95869800-95877400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:95869800-95877400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:95870000-95872400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr9:95870000-95872600	Weak transcription	Esophagus	oesophagus
34	chr9:95870000-95876600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:95870200-95872800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:95870200-95876400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:95870200-95877400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:95870400-95872400	Weak transcription	Brain Substantia Nigra	brain
40	chr9:95870400-95872600	Weak transcription	Aorta	Aorta
41	chr9:95870400-95873000	Weak transcription	Left Ventricle	heart
42	chr9:95870600-95873600	Strong transcription	NHEK	skin
43	chr9:95870600-95875000	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr9:95870800-95873800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr9:95871000-95872800	Genic enhancers	Adipose Nuclei	Adipose
46	chr9:95871000-95894200	Weak transcription	Dnd41	blood
47	chr9:95871200-95872400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:95871200-95872400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:95871200-95872600	Weak transcription	Brain Anterior Caudate	brain
50	chr9:95871200-95872600	Weak transcription	Rectal Mucosa Donor 31	rectum

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