Variant report

Variant	rs3789254
Chromosome Location	chr9:116131580-116131581
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116129698..116134206-chr9:116137986..116141026,4	K562	blood:
2	chr9:116129075..116133029-chr9:116162215..116166672,4	K562	blood:
3	chr9:116129674..116142040-chr9:116159218..116175468,34	MCF-7	breast:
4	chr9:116119995..116122506-chr9:116129873..116132566,2	MCF-7	breast:
5	chr9:116129961..116132443-chr9:116136297..116137868,2	K562	blood:
6	chr9:116125138..116127996-chr9:116129478..116132469,3	K562	blood:
7	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
8	chr9:116129585..116133857-chr9:116136214..116139486,5	K562	blood:
9	chr9:116124299..116128919-chr9:116129296..116133206,5	K562	blood:
10	chr9:116129625..116132113-chr9:116158128..116160524,2	MCF-7	breast:
11	chr9:116079936..116083155-chr9:116131441..116134734,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000148229	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000119431	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10481674	1.00[CHB][hapmap]
rs10981733	1.00[CHB][hapmap]
rs10981743	1.00[CHB][hapmap]
rs10981745	1.00[CHB][hapmap]
rs10981746	1.00[CHB][hapmap]
rs10981747	1.00[CHB][hapmap]
rs10981748	1.00[CHB][hapmap]
rs10981760	0.85[ASN][1000 genomes]
rs12006029	1.00[CHB][hapmap]
rs12337552	1.00[CHB][hapmap]
rs1543535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16932583	1.00[CHB][hapmap]
rs17764563	1.00[CHB][hapmap]
rs28495580	0.85[ASN][1000 genomes]
rs28607343	0.85[ASN][1000 genomes]
rs3750529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437724	1.00[CHB][hapmap]
rs4442214	1.00[CHB][hapmap]
rs4636275	1.00[CHB][hapmap]
rs60528957	0.85[ASN][1000 genomes]
rs66649870	0.85[ASN][1000 genomes]
rs7865438	1.00[CHB][hapmap]
rs7875945	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv519849	chr9:116111407-116144973	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1036586	chr9:116118902-116136993	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv615214	chr9:116125789-116149967	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116113000-116135600	Weak transcription	Colonic Mucosa	Colon
2	chr9:116113000-116138000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:116113400-116135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:116113800-116137800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:116114200-116136400	Weak transcription	Primary B cells from cord blood	blood
6	chr9:116115400-116135000	Weak transcription	Esophagus	oesophagus
7	chr9:116115600-116132800	Weak transcription	Fetal Intestine Large	intestine
8	chr9:116116400-116137000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:116120200-116131800	Weak transcription	Lung	lung
10	chr9:116123000-116132800	Weak transcription	Fetal Stomach	stomach
11	chr9:116123200-116131800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:116123200-116136400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:116123600-116138200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:116124000-116135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:116124000-116135000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:116124000-116135600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:116124000-116135600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:116124400-116131600	Weak transcription	Pancreas	Pancrea
19	chr9:116124400-116135600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:116124800-116134200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:116124800-116134400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:116124800-116135000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:116124800-116135200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:116124800-116135400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:116124800-116135800	Weak transcription	Brain Substantia Nigra	brain
26	chr9:116125000-116138000	Weak transcription	Fetal Kidney	kidney
27	chr9:116125200-116133600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:116125200-116135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:116126200-116134400	Weak transcription	Placenta	Placenta
30	chr9:116126800-116133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:116127800-116160400	Weak transcription	Fetal Heart	heart
32	chr9:116128000-116135000	Weak transcription	Left Ventricle	heart
33	chr9:116128000-116135200	Weak transcription	Adipose Nuclei	Adipose
34	chr9:116128200-116137200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:116128400-116135400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:116128600-116135000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:116128800-116135000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr9:116128800-116135800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr9:116128800-116137600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:116129000-116135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:116129200-116132000	Enhancers	HepG2	liver
42	chr9:116129200-116134400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:116129200-116135000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:116129200-116137600	Weak transcription	Hela-S3	cervix
45	chr9:116129400-116131800	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:116129800-116131600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:116130200-116132000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:116130200-116132400	Strong transcription	Fetal Intestine Small	intestine
49	chr9:116130400-116132600	Enhancers	Stomach Mucosa	stomach
50	chr9:116130600-116131800	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links