Variant report

Variant	rs10123848
Chromosome Location	chr9:71161504-71161505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr9:71161259-71162231	GM12878	blood:	n/a	chr9:71161371-71161388 chr9:71161372-71161388
2	PAX5	chr9:71161295-71162187	GM12878	blood:	n/a	chr9:71161613-71161622 chr9:71161894-71161903
3	SPI1	chr9:71161392-71162102	GM12878	blood:	n/a	chr9:71161893-71161906
4	RUNX3	chr9:71161269-71162133	GM12878	blood:	n/a	n/a
5	BCLAF1	chr9:71161350-71162066	GM12878	blood:	n/a	n/a
6	TCF3	chr9:71161379-71161996	GM12878	blood:	n/a	n/a
7	SPI1	chr9:71161491-71161973	GM12878	blood:	n/a	chr9:71161893-71161906
8	RELA	chr9:71161409-71162046	GM19193	blood:	n/a	n/a
9	ATF2	chr9:71161302-71162158	GM12878	blood:	n/a	n/a
10	EP300	chr9:71161396-71162074	GM12878	blood:	n/a	chr9:71161895-71161904 chr9:71161917-71161927
11	SPI1	chr9:71161413-71162153	GM12891	blood:	n/a	chr9:71161893-71161906
12	USF2	chr9:71161428-71161588	HepG2	liver:	n/a	n/a
13	EBF1	chr9:71161488-71161972	GM12878	blood:	n/a	n/a
14	SPI1	chr9:71161497-71161942	HL-60	blood:	n/a	chr9:71161893-71161906
15	MAX	chr9:71161420-71161961	NB4	blood:	n/a	chr9:71161581-71161591
16	POLR2A	chr9:71161427-71162118	GM12892	blood:	n/a	n/a
17	NFATC1	chr9:71161345-71162134	GM12878	blood:	n/a	n/a
18	BHLHE40	chr9:71161459-71162275	GM12878	blood:	n/a	n/a
19	BCL11A	chr9:71161433-71162084	GM12878	blood:	n/a	n/a
20	MEF2A	chr9:71161411-71162088	GM12878	blood:	n/a	n/a
21	EBF1	chr9:71161395-71162149	GM12878	blood:	n/a	n/a
22	NFYB	chr9:71161376-71161955	GM12878	blood:	n/a	n/a
23	ATF2	chr9:71161342-71162104	GM12878	blood:	n/a	n/a
24	POU2F2	chr9:71161341-71162025	GM12891	blood:	n/a	n/a
25	MTA3	chr9:71161220-71162253	GM12878	blood:	n/a	n/a
26	RUNX3	chr9:71161274-71162161	GM12878	blood:	n/a	n/a
27	BATF	chr9:71161399-71162069	GM12878	blood:	n/a	n/a
28	RELA	chr9:71161384-71162103	GM18951	blood:	n/a	n/a
29	PML	chr9:71161285-71162092	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:71161322-71161966	HL-60	blood:	n/a	n/a
31	EP300	chr9:71161410-71162087	GM12878	blood:	n/a	chr9:71161895-71161904 chr9:71161917-71161927
32	SPI1	chr9:71161314-71162171	GM12878	blood:	n/a	chr9:71161893-71161906
33	MYC	chr9:71161431-71161987	NB4	blood:	n/a	chr9:71161581-71161591
34	POLR2A	chr9:71161413-71162010	HL-60	blood:	n/a	n/a
35	POU2F2	chr9:71161382-71162064	GM12891	blood:	n/a	n/a
36	PAX5	chr9:71161300-71162121	GM12878	blood:	n/a	chr9:71161613-71161622 chr9:71161894-71161903
37	POLR2A	chr9:71161284-71161767	GM12878	blood:	n/a	n/a
38	NFATC1	chr9:71161441-71162099	GM12878	blood:	n/a	n/a
39	ELF1	chr9:71161379-71162132	GM12878	blood:	n/a	chr9:71161610-71161621 chr9:71161895-71161906
40	WRNIP1	chr9:71161430-71161953	GM12878	blood:	n/a	n/a
41	NFIC	chr9:71161350-71162230	GM12878	blood:	n/a	chr9:71161371-71161388 chr9:71161372-71161388
42	BCLAF1	chr9:71161347-71162166	GM12878	blood:	n/a	n/a
43	RCOR1	chr9:71161438-71162098	GM12878	blood:	n/a	n/a
44	EP300	chr9:71161489-71162070	GM12878	blood:	n/a	chr9:71161895-71161904 chr9:71161917-71161927
45	PAX5	chr9:71161387-71162089	GM12878	blood:	n/a	chr9:71161613-71161622 chr9:71161894-71161903
46	CEBPB	chr9:71161273-71162165	GM12878	blood:	n/a	n/a
47	IRF4	chr9:71161316-71162137	GM12878	blood:	n/a	n/a
48	BATF	chr9:71161338-71162104	GM12878	blood:	n/a	n/a
49	SPI1	chr9:71161368-71162160	GM12891	blood:	n/a	chr9:71161893-71161906
50	EBF1	chr9:71161435-71162095	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf71-1	chr9:71161475-71161505	XLOC_007722
2	lnc-C9orf71-1	chr9:71161475-71161518	NR_109769

Variant related genes	Relation type
ENSG00000234506	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10114981	0.81[AFR][1000 genomes]
rs10120745	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10123762	0.84[AFR][1000 genomes]
rs10124105	0.89[AFR][1000 genomes]
rs10511957	1.00[CHB][hapmap]
rs10511958	0.82[CEU][hapmap]
rs10780960	0.82[CEU][hapmap]
rs10868879	1.00[CEU][hapmap]
rs10868922	0.81[AMR][1000 genomes]
rs10869040	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142616	0.81[AMR][1000 genomes]
rs11142714	1.00[YRI][hapmap]
rs11789244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11790064	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792137	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11794424	1.00[CHB][hapmap]
rs11795356	0.87[AMR][1000 genomes]
rs12238439	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12341862	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12342668	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12348463	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12349403	0.89[AFR][1000 genomes]
rs12351373	1.00[YRI][hapmap]
rs12552415	1.00[YRI][hapmap]
rs1353009	0.82[CEU][hapmap]
rs1353010	1.00[CEU][hapmap]
rs17053702	1.00[CHB][hapmap]
rs17054803	1.00[CHB][hapmap]
rs17059173	1.00[CHB][hapmap]
rs265087	0.82[CEU][hapmap]
rs28373225	0.96[AFR][1000 genomes]
rs28685588	0.89[AFR][1000 genomes]
rs4237244	0.87[EUR][1000 genomes]
rs4745041	0.82[CEU][hapmap]
rs6560144	0.82[CEU][hapmap]
rs7039686	0.82[CEU][hapmap]
rs7042123	1.00[CEU][hapmap]
rs73449507	0.96[AFR][1000 genomes]
rs7855134	0.82[CEU][hapmap]
rs7866604	1.00[CHB][hapmap]

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	nsv893413	chr9:71130848-71196984	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893411	chr9:71130848-71199545	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv893412	chr9:71130848-71199545	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1024967	chr9:71130848-71210031	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv482506	chr9:71130848-71280888	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv466392	chr9:71130848-71318817	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv614546	chr9:71130848-71318817	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1026962	chr9:71130848-71357605	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv893414	chr9:71139378-71320732	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71139600-71161600	Weak transcription	Spleen	Spleen
2	chr9:71145800-71161600	Weak transcription	Gastric	stomach
3	chr9:71152200-71161600	Weak transcription	Right Ventricle	heart
4	chr9:71152200-71170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:71153800-71161800	Weak transcription	Psoas Muscle	Psoas
6	chr9:71154200-71161600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:71156600-71161600	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:71156600-71161600	Weak transcription	HepG2	liver
9	chr9:71157200-71165600	Weak transcription	Stomach Mucosa	stomach
10	chr9:71157200-71166000	Weak transcription	Colonic Mucosa	Colon
11	chr9:71157400-71166000	Weak transcription	Fetal Heart	heart
12	chr9:71158200-71161600	Weak transcription	Fetal Intestine Large	intestine
13	chr9:71159800-71163800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr9:71160400-71162000	Flanking Active TSS	GM12878-XiMat	blood
15	chr9:71160400-71163200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr9:71160400-71164000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr9:71160600-71162200	Enhancers	Small Intestine	intestine
18	chr9:71161000-71162200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:71161200-71162400	Enhancers	Right Atrium	heart
20	chr9:71161200-71163600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr9:71161400-71161600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:71161400-71161800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:71161400-71161800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr9:71161400-71161800	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr9:71161400-71161800	Flanking Active TSS	Fetal Kidney	kidney
26	chr9:71161400-71161800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr9:71161400-71161800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr9:71161400-71162000	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr9:71161400-71162000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:71161400-71162000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr9:71161400-71162000	Enhancers	Rectal Smooth Muscle	rectum
32	chr9:71161400-71162200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr9:71161400-71162200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:71161400-71162200	Enhancers	Colon Smooth Muscle	Colon
35	chr9:71161400-71162200	Enhancers	Fetal Intestine Small	intestine
36	chr9:71161400-71162200	Enhancers	Left Ventricle	heart
37	chr9:71161400-71162200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr9:71161400-71162200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr9:71161400-71162600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr9:71161400-71163600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:71161400-71163800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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