Variant report

Variant	rs12349786
Chromosome Location	chr9:6905429-6905430
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6755920..6758663-chr9:6904149..6906669,2	K562	blood:

Variant related genes	Relation type
ENSG00000107077	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10114023	0.83[YRI][hapmap]
rs10117564	0.91[YRI][hapmap];0.85[AMR][1000 genomes]
rs10120163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10122648	0.85[AFR][1000 genomes]
rs10125702	0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10975902	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs10975903	0.86[EUR][1000 genomes]
rs10975904	0.86[EUR][1000 genomes]
rs10975905	0.86[EUR][1000 genomes]
rs10975906	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs10975908	0.86[EUR][1000 genomes]
rs10975922	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs12349290	0.86[EUR][1000 genomes]
rs12686310	0.86[EUR][1000 genomes]
rs28412017	0.90[ASN][1000 genomes]
rs28469195	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56808908	0.86[EUR][1000 genomes]
rs57054567	0.86[EUR][1000 genomes]
rs59139150	0.86[EUR][1000 genomes]
rs61700387	0.86[EUR][1000 genomes]
rs7869241	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	esv2752309	chr9:6670448-6908200	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
9	nsv870332	chr9:6694842-6911550	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv1016109	chr9:6712314-6924843	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6869600-6909400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:6869800-6908000	Weak transcription	Fetal Stomach	stomach
3	chr9:6880800-6907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:6882800-6912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:6883000-6911800	Weak transcription	Psoas Muscle	Psoas
6	chr9:6887600-6911800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:6889600-6929000	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:6890000-6912000	Weak transcription	Spleen	Spleen
9	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
10	chr9:6890400-6911400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:6891800-6907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:6893000-6909400	Strong transcription	Primary B cells from cord blood	blood
13	chr9:6893800-6908200	Weak transcription	Colonic Mucosa	Colon
14	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:6894000-6921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:6894400-6906800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:6894800-6911800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:6894800-6912000	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:6894800-6922000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:6894800-6931600	Weak transcription	Dnd41	blood
21	chr9:6895600-6919800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr9:6897000-6911800	Weak transcription	Pancreas	Pancrea
24	chr9:6897600-6932200	Weak transcription	Small Intestine	intestine
25	chr9:6898200-6911800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr9:6898200-6911800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:6898200-6911800	Weak transcription	Stomach Mucosa	stomach
28	chr9:6898200-6921200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr9:6898200-6928800	Weak transcription	Ovary	ovary
30	chr9:6898200-6930800	Weak transcription	HSMMtube	muscle
31	chr9:6898400-6912000	Weak transcription	Brain Anterior Caudate	brain
32	chr9:6899000-6905600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr9:6900000-6906600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr9:6900000-6921200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr9:6900400-6905800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:6900600-6943000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:6901600-6906200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:6901600-6908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:6901600-6917400	Weak transcription	Thymus	Thymus
40	chr9:6901600-6944200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:6901800-6907000	Enhancers	HepG2	liver
42	chr9:6901800-6922000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:6901800-6931600	Weak transcription	Fetal Intestine Large	intestine
44	chr9:6902000-6913400	Weak transcription	K562	blood
45	chr9:6902000-6923800	Weak transcription	Fetal Intestine Small	intestine
46	chr9:6902600-6911800	Weak transcription	Right Atrium	heart
47	chr9:6902800-6906200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr9:6902800-6906400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:6902800-6906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr9:6902800-6907400	Weak transcription	Hela-S3	cervix

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