Variant report

Variant	rs3131899
Chromosome Location	chr9:97025979-97025980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96928568..96930309-chr9:97024360..97026072,2	K562	blood:
2	chr9:97020642..97023033-chr9:97025646..97027607,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction
ENSG00000175787	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10821325	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10821326	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10993124	0.89[ASN][1000 genomes]
rs16912862	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2479602	0.86[CHD][hapmap];1.00[MKK][hapmap]
rs3118753	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3118754	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3118756	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3118761	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3118762	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3118765	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3131901	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3131902	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3131904	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3131910	0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs36064675	0.83[ASN][1000 genomes]
rs4744329	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4744346	0.86[CHD][hapmap];1.00[MKK][hapmap]
rs62578820	0.89[ASN][1000 genomes]
rs6479533	0.81[ASN][1000 genomes]
rs6479534	0.81[ASN][1000 genomes]
rs688165	0.86[CHD][hapmap];1.00[MKK][hapmap]
rs7027606	0.81[JPT][hapmap]
rs7041842	0.81[ASN][1000 genomes]
rs9409511	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9409512	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs9409513	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9695176	0.81[ASN][1000 genomes]
rs9696843	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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 miRNA target site	218 gene(s)	inside rSNPs	diseases
2	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases
3	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
5	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97022000-97028600	Weak transcription	Small Intestine	intestine
2	chr9:97022200-97026200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:97022200-97028400	Weak transcription	Fetal Intestine Small	intestine
4	chr9:97022200-97028400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:97022200-97028600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:97022200-97031400	Weak transcription	Left Ventricle	heart
7	chr9:97022200-97031600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:97022200-97031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:97022200-97031600	Weak transcription	HSMMtube	muscle
10	chr9:97022200-97033400	Weak transcription	Fetal Stomach	stomach
11	chr9:97022200-97040800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:97022200-97041800	Weak transcription	Fetal Lung	lung
13	chr9:97022200-97042600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
15	chr9:97022400-97026400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:97022400-97026600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:97022400-97028600	Weak transcription	Fetal Intestine Large	intestine
18	chr9:97022400-97031400	Weak transcription	NHEK	skin
19	chr9:97022400-97036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:97022600-97026400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:97022600-97026400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:97022600-97027800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:97022600-97028600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr9:97022600-97028800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:97022600-97029200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:97022600-97040600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:97022800-97028600	Weak transcription	Primary B cells from cord blood	blood
29	chr9:97022800-97029200	Weak transcription	HSMM	muscle
30	chr9:97022800-97031400	Weak transcription	Psoas Muscle	Psoas
31	chr9:97022800-97040800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:97022800-97040800	Weak transcription	Thymus	Thymus
33	chr9:97022800-97042400	Weak transcription	Brain Angular Gyrus	brain
34	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
35	chr9:97023000-97026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:97023000-97026200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:97023000-97026200	Weak transcription	Dnd41	blood
38	chr9:97023000-97026200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr9:97023000-97026400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:97023000-97026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:97023000-97026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:97023000-97027800	Weak transcription	Stomach Mucosa	stomach
43	chr9:97023000-97028200	Weak transcription	HepG2	liver
44	chr9:97023000-97028400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr9:97023000-97028400	Weak transcription	A549	lung
46	chr9:97023000-97029000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:97023000-97029200	Weak transcription	Spleen	Spleen
48	chr9:97023000-97029800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr9:97023000-97030000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:97023000-97031600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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