Variant report

Variant	rs12378370
Chromosome Location	chr9:95826971-95826972
allele	C/G
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	MYC	chr9:95826730-95827069	K562	blood:	n/a	n/a
2	POLR2A	chr9:95826580-95827196	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:95826489-95827220	GM12878	blood:	n/a	n/a
4	GABPA	chr9:95826652-95827043	K562	blood:	n/a	chr9:95826963-95826972
5	NR2F2	chr9:95826645-95827058	K562	blood:	n/a	n/a
6	ZMIZ1	chr9:95826627-95827048	K562	blood:	n/a	n/a
7	CTCF	chr9:95826890-95827050	GM19239	blood:	n/a	n/a
8	RCOR1	chr9:95826619-95827205	GM12878	blood:	n/a	n/a
9	SRF	chr9:95826744-95827006	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:95826506-95827217	GM18951	blood:	n/a	n/a
11	RCOR1	chr9:95826744-95827099	K562	blood:	n/a	n/a
12	TEAD4	chr9:95826701-95826993	K562	blood:	n/a	n/a
13	MXI1	chr9:95826601-95827161	GM12878	blood:	n/a	n/a
14	PAX5	chr9:95826627-95827052	GM12878	blood:	n/a	chr9:95827002-95827011
15	CTCF	chr9:95826733-95827019	GM12878	blood:	n/a	chr9:95826761-95826769
16	SPI1	chr9:95826635-95827144	GM12891	blood:	n/a	chr9:95827002-95827009
17	ELF1	chr9:95826470-95827454	GM12878	blood:	n/a	n/a
18	CCNT2	chr9:95826690-95827103	K562	blood:	n/a	n/a
19	POLR2A	chr9:95825693-95827281	GM12878	blood:	n/a	n/a
20	ZEB1	chr9:95826536-95827109	GM12878	blood:	n/a	n/a
21	POU2F2	chr9:95826546-95827303	GM12891	blood:	n/a	n/a
22	POLR2A	chr9:95826597-95827064	GM12891	blood:	n/a	n/a
23	ZNF143	chr9:95826527-95827071	GM12878	blood:	n/a	n/a
24	ESRRA	chr9:95825379-95827466	GM12878	blood:	n/a	chr9:95826281-95826295 chr9:95826280-95826296 chr9:95826863-95826879 chr9:95826863-95826879 chr9:95826279-95826297 chr9:95825948-95825958 chr9:95826735-95826751 chr9:95826281-95826300
25	NRF1	chr9:95826667-95827156	GM12878	blood:	n/a	chr9:95826963-95826972
26	PAX5	chr9:95826477-95827256	GM12878	blood:	n/a	chr9:95827002-95827011
27	ATF2	chr9:95826593-95827132	GM12878	blood:	n/a	n/a
28	PML	chr9:95826453-95827494	GM12878	blood:	n/a	chr9:95827238-95827246
29	TBP	chr9:95826831-95827031	K562	blood:	n/a	n/a
30	POU2F2	chr9:95826587-95827046	GM12891	blood:	n/a	n/a
31	MYC	chr9:95826645-95827076	K562	blood:	n/a	n/a
32	ATF1	chr9:95826674-95827190	K562	blood:	n/a	n/a
33	ETS1	chr9:95826559-95827027	GM12878	blood:	n/a	chr9:95826968-95826979 chr9:95827003-95827010 chr9:95826823-95826834 chr9:95827001-95827014
34	POLR2A	chr9:95826606-95827259	HL-60	blood:	n/a	n/a
35	PAX5	chr9:95826713-95827023	GM12878	blood:	n/a	chr9:95827002-95827011
36	BCLAF1	chr9:95826541-95827104	GM12878	blood:	n/a	chr9:95826966-95826979
37	MAFF	chr9:95826786-95827095	K562	blood:	n/a	n/a
38	ZNF143	chr9:95826625-95827073	K562	blood:	n/a	n/a
39	CBX3	chr9:95826527-95827169	K562	blood:	n/a	n/a
40	HCFC1	chr9:95826708-95827109	K562	blood:	n/a	n/a
41	EBF1	chr9:95826599-95827043	GM12878	blood:	n/a	n/a
42	MAX	chr9:95826606-95827145	K562	blood:	n/a	chr9:95826643-95826652
43	MAX	chr9:95826778-95826979	K562	blood:	n/a	n/a
44	YY1	chr9:95826641-95827124	GM12892	blood:	n/a	n/a
45	MAZ	chr9:95826634-95827139	K562	blood:	n/a	chr9:95826643-95826652
46	SRF	chr9:95826664-95827039	K562	blood:	n/a	n/a
47	STAT5A	chr9:95826596-95827037	GM12878	blood:	n/a	chr9:95827004-95827011
48	YY1	chr9:95826789-95826999	K562	blood:	n/a	n/a
49	BHLHE40	chr9:95826663-95827290	K562	blood:	n/a	chr9:95826966-95826982
50	POLR2A	chr9:95826846-95827107	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95826956..95829616-chr9:95830971..95832502,2	K562	blood:
2	chr9:95824581..95826118-chr9:95826533..95829514,2	MCF-7	breast:
3	chr9:95819521..95827100-chr9:95855273..95859349,14	K562	blood:
4	chr9:95819208..95822509-chr9:95822531..95826993,4	K562	blood:
5	chr9:95825270..95827646-chr9:95832621..95835628,3	K562	blood:

Variant related genes	Relation type
SUSD3	TF binding region
ENSG00000223446	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000157303	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10761192	0.81[EUR][1000 genomes]
rs10821061	0.95[ASN][1000 genomes]
rs10821064	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34105406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95820800-95827600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr9:95821000-95827400	Flanking Active TSS	GM12878-XiMat	blood
3	chr9:95821600-95827400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr9:95821600-95827600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr9:95821800-95827400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr9:95822000-95834200	Weak transcription	Esophagus	oesophagus
7	chr9:95822000-95834200	Weak transcription	Right Atrium	heart
8	chr9:95822400-95828600	Enhancers	Primary hematopoietic stem cells	blood
9	chr9:95822600-95834400	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:95822800-95831000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:95823400-95827800	Weak transcription	Right Ventricle	heart
12	chr9:95824000-95827000	Weak transcription	Placenta	Placenta
13	chr9:95824000-95833800	Weak transcription	Ovary	ovary
14	chr9:95824200-95827200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:95824400-95827200	Weak transcription	Lung	lung
16	chr9:95824600-95854000	Weak transcription	Gastric	stomach
17	chr9:95824800-95827000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:95824800-95833200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:95825000-95827000	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:95825200-95827000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:95825200-95829000	Weak transcription	Pancreas	Pancrea
22	chr9:95825200-95834000	Weak transcription	Liver	Liver
23	chr9:95825400-95827600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr9:95825400-95828200	Enhancers	Duodenum Mucosa	Duodenum
25	chr9:95825600-95827400	Enhancers	K562	blood
26	chr9:95825600-95827800	Enhancers	Spleen	Spleen
27	chr9:95825800-95827000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:95825800-95828600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr9:95826000-95827400	Flanking Active TSS	Dnd41	blood
30	chr9:95826000-95827800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr9:95826200-95827000	Active TSS	Colonic Mucosa	Colon
32	chr9:95826200-95827200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr9:95826200-95827200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:95826200-95827400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:95826200-95828000	Weak transcription	Brain Substantia Nigra	brain
36	chr9:95826200-95828400	Strong transcription	Fetal Intestine Small	intestine
37	chr9:95826400-95827000	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr9:95826400-95827000	Active TSS	Thymus	Thymus
39	chr9:95826400-95828400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr9:95826600-95827000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr9:95826600-95827000	Active TSS	Primary T cells from cord blood	blood
42	chr9:95826600-95827200	Enhancers	HSMM	muscle
43	chr9:95826600-95827400	Flanking Active TSS	Fetal Thymus	thymus
44	chr9:95826600-95828000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr9:95826600-95828200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:95826600-95828200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr9:95826600-95828400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:95826800-95827000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr9:95826800-95827000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:95826800-95827000	Flanking Active TSS	Primary B cells from cord blood	blood

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