Variant report

Variant	rs7850317
Chromosome Location	chr9:2809548-2809549
allele	A/C
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	TCF12	chr9:2809447-2810598	SK-N-SH	brain:	n/a	chr9:2810285-2810293
2	JUND	chr9:2809538-2810309	SK-N-SH	brain:	n/a	chr9:2810116-2810125 chr9:2810115-2810124
3	EP300	chr9:2809533-2810650	A549	lung:	n/a	chr9:2810132-2810146
4	TCF12	chr9:2809483-2810697	A549	lung:	n/a	chr9:2810285-2810293
5	SIN3A	chr9:2809428-2810334	H1-hESC	embryonic stem cell:	n/a	chr9:2809793-2809801 chr9:2810109-2810122
6	SP1	chr9:2809539-2810498	H1-hESC	embryonic stem cell:	n/a	n/a
7	PBX3	chr9:2809320-2810527	SK-N-SH	brain:	n/a	chr9:2809551-2809571
8	PBX3	chr9:2809445-2810427	SK-N-SH	brain:	n/a	chr9:2809551-2809571
9	CEBPB	chr9:2809402-2810317	IMR90	lung:	n/a	n/a
10	GATA3	chr9:2809411-2810936	SK-N-SH	brain:	n/a	chr9:2810521-2810533 chr9:2810643-2810652 chr9:2810524-2810534 chr9:2810522-2810532 chr9:2810519-2810535 chr9:2810524-2810531 chr9:2810522-2810531
11	POLR2A	chr9:2809115-2809924	IMR90	lung:	n/a	n/a
12	MAZ	chr9:2809490-2810526	IMR90	lung:	n/a	chr9:2810113-2810123 chr9:2810103-2810113
13	TEAD4	chr9:2809465-2810644	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr9:2809515-2810079	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr9:2809426-2810928	A549	lung:	n/a	chr9:2810521-2810533 chr9:2810643-2810652 chr9:2810524-2810534 chr9:2810522-2810532 chr9:2810519-2810535 chr9:2810524-2810531 chr9:2810522-2810531
16	SP1	chr9:2809523-2810506	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr9:2809411-2810137	H1-hESC	embryonic stem cell:	n/a	n/a
18	ATF2	chr9:2809529-2810086	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF12	chr9:2809410-2810572	SK-N-SH	brain:	n/a	chr9:2810285-2810293
20	EP300	chr9:2809493-2810706	A549	lung:	n/a	chr9:2810132-2810146
21	NFIC	chr9:2809434-2810633	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr9:2809466-2810602	H1-hESC	embryonic stem cell:	n/a	n/a
23	GATA3	chr9:2809526-2810970	SK-N-SH	brain:	n/a	chr9:2810521-2810533 chr9:2810643-2810652 chr9:2810524-2810534 chr9:2810522-2810532 chr9:2810519-2810535 chr9:2810524-2810531 chr9:2810522-2810531
24	CEBPB	chr9:2809426-2810086	HepG2	liver:	n/a	n/a
25	POLR2A	chr9:2809393-2812119	HepG2	liver:	n/a	n/a
26	EP300	chr9:2809506-2810619	SK-N-SH	brain:	n/a	chr9:2810132-2810146
27	JUND	chr9:2809548-2810417	H1-hESC	embryonic stem cell:	n/a	chr9:2810116-2810125 chr9:2810115-2810124

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2808764..2811961-chr9:2812459..2815898,4	K562	blood:

Variant related genes	Relation type
KIAA0020	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10125846	0.90[CHB][hapmap]
rs2292000	0.81[CHB][hapmap]
rs3739460	0.95[CHB][hapmap]
rs3824350	0.81[CHB][hapmap]
rs3858032	0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv892082	chr9:2699606-2833267	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2787800-2812200	Strong transcription	Fetal Muscle Trunk	muscle
2	chr9:2791600-2815800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:2791800-2821800	Strong transcription	Primary T cells from cord blood	blood
4	chr9:2792000-2822200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:2792200-2813000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:2792800-2809600	Strong transcription	Liver	Liver
7	chr9:2793200-2826600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:2793400-2814200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr9:2794400-2814800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:2795200-2817600	Weak transcription	Stomach Mucosa	stomach
11	chr9:2795400-2814000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr9:2795800-2809800	Strong transcription	Fetal Intestine Large	intestine
13	chr9:2796400-2822200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:2796600-2813200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr9:2796800-2812600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr9:2797600-2813400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr9:2797600-2813600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr9:2797800-2813000	Strong transcription	Dnd41	blood
19	chr9:2797800-2813800	Strong transcription	Primary B cells from cord blood	blood
20	chr9:2797800-2813800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:2798000-2837400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:2798400-2812600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr9:2798800-2811600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:2800200-2812000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:2801200-2812200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr9:2801200-2813800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:2801200-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:2801400-2813800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:2801600-2837200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:2801800-2814200	Strong transcription	HMEC	breast
31	chr9:2802200-2809800	Weak transcription	Colonic Mucosa	Colon
32	chr9:2802400-2814200	Strong transcription	GM12878-XiMat	blood
33	chr9:2803000-2810600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:2803200-2814000	Strong transcription	NHEK	skin
35	chr9:2803600-2812000	Strong transcription	HUVEC	blood vessel
36	chr9:2803600-2829200	Weak transcription	Small Intestine	intestine
37	chr9:2803800-2809600	Strong transcription	Hela-S3	cervix
38	chr9:2804000-2810800	Weak transcription	Gastric	stomach
39	chr9:2804200-2810200	Weak transcription	Brain Germinal Matrix	brain
40	chr9:2804400-2813800	Strong transcription	K562	blood
41	chr9:2805200-2810600	Weak transcription	Esophagus	oesophagus
42	chr9:2805400-2809800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:2805400-2810400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:2805400-2810800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:2805800-2829400	Weak transcription	Fetal Brain Male	brain
46	chr9:2807000-2810400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr9:2807000-2812000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr9:2807000-2812200	Strong transcription	Fetal Thymus	thymus
49	chr9:2807400-2811600	Strong transcription	Fetal Brain Female	brain
50	chr9:2807600-2811600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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