Variant report

Variant	rs61700387
Chromosome Location	chr9:6923722-6923723
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	MXI1	chr9:6923717-6925962	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr9:6923633-6923754	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6921809..6924418-chr9:6928929..6932002,3	MCF-7	breast:

Variant related genes	Relation type
KDM4C	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10120163	0.86[EUR][1000 genomes]
rs10125216	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10125702	0.86[EUR][1000 genomes]
rs10815484	0.93[ASN][1000 genomes]
rs10815485	0.93[ASN][1000 genomes]
rs10975902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10975903	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10975904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10975905	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10975906	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10975908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10975913	0.91[ASN][1000 genomes]
rs10975921	0.85[ASN][1000 genomes]
rs10975922	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10975931	0.80[AMR][1000 genomes]
rs12349290	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12349786	0.86[EUR][1000 genomes]
rs12686310	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28412017	0.83[EUR][1000 genomes]
rs28469195	0.86[EUR][1000 genomes]
rs28632803	0.80[AMR][1000 genomes]
rs56808908	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57054567	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58288912	0.80[AMR][1000 genomes]
rs59139150	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60170601	0.80[AMR][1000 genomes]
rs7862859	0.93[ASN][1000 genomes]
rs7869241	0.86[EUR][1000 genomes]
rs7876040	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv892184	chr9:6906384-6985602	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6889600-6929000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
3	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:6894800-6931600	Weak transcription	Dnd41	blood
5	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr9:6897600-6932200	Weak transcription	Small Intestine	intestine
7	chr9:6898200-6928800	Weak transcription	Ovary	ovary
8	chr9:6898200-6930800	Weak transcription	HSMMtube	muscle
9	chr9:6900600-6943000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:6901600-6944200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:6901800-6931600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:6902000-6923800	Weak transcription	Fetal Intestine Small	intestine
13	chr9:6902800-6931000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:6903000-6938600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr9:6906400-6933200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:6906600-6938200	Weak transcription	Adipose Nuclei	Adipose
17	chr9:6908800-6942600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:6912200-6923800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr9:6912400-6923800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:6912400-6923800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:6912400-6927200	Weak transcription	Psoas Muscle	Psoas
22	chr9:6912400-6930800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:6912400-6931000	Weak transcription	Right Ventricle	heart
24	chr9:6912400-6931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:6912400-6932200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:6912400-6932200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:6912400-6932200	Weak transcription	Spleen	Spleen
28	chr9:6912400-6978400	Weak transcription	Esophagus	oesophagus
29	chr9:6912600-6924400	Weak transcription	Brain Substantia Nigra	brain
30	chr9:6912600-6925200	Weak transcription	Fetal Brain Male	brain
31	chr9:6912600-6925400	Weak transcription	Left Ventricle	heart
32	chr9:6912600-6926000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:6912600-6929600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:6913800-6925000	Weak transcription	K562	blood
35	chr9:6915800-6925400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:6916000-6925800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:6916000-6932200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:6920200-6924400	Weak transcription	Stomach Mucosa	stomach
39	chr9:6920200-6928800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:6920200-6930000	Weak transcription	HSMM	muscle
41	chr9:6920200-6930800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:6920200-6931000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:6920200-6931000	Weak transcription	Fetal Muscle Leg	muscle
44	chr9:6920400-6931000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:6920600-6926800	Strong transcription	Primary T cells from cord blood	blood
46	chr9:6921000-6924600	Strong transcription	Fetal Thymus	thymus
47	chr9:6921400-6924200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr9:6921400-6934000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:6921600-6923800	Weak transcription	Liver	Liver
50	chr9:6921600-6925800	Enhancers	Primary neutrophils fromperipheralblood	blood

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