Variant report

Variant	rs658123
Chromosome Location	chr9:3271914-3271915
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	USF1	chr9:3271639-3271964	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RFX3	TF binding region

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10429463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1147822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11998979	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12004313	0.84[EUR][1000 genomes]
rs12004744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13296552	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs1443205	0.92[CEU][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs16916423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17658724	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17658838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.92[EUR][1000 genomes]
rs17715051	0.84[CEU][hapmap]
rs17715160	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17715317	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2274487	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2304928	0.82[EUR][1000 genomes]
rs2920363	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920369	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2920370	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2920375	0.84[EUR][1000 genomes]
rs2920376	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2920377	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2920378	0.88[CHB][hapmap]
rs2920379	0.88[CHB][hapmap]
rs2920380	0.88[CHB][hapmap]
rs2920381	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2920382	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2986678	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2986679	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2986680	0.88[CHB][hapmap]
rs2986684	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2986686	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs2986687	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2986688	0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs2986690	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2986691	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2986693	0.91[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs2986694	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs2986695	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2986696	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2986697	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2986698	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2986700	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs2986701	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2991297	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2991298	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2991300	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs2991301	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs2991302	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2991304	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2991305	0.91[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2991306	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2991307	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2991308	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs2991309	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2991310	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2991311	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap]
rs2991314	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2991315	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2991317	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2991318	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2991319	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2991320	0.88[CHB][hapmap]
rs2991321	0.88[CHB][hapmap]
rs2991322	0.88[CHB][hapmap]
rs2991323	0.88[CHB][hapmap]
rs3012670	0.88[CHB][hapmap]
rs3012672	0.88[CHB][hapmap]
rs3012680	0.91[ASN][1000 genomes]
rs3012686	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3012688	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3012692	0.92[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs3012693	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs3012694	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs3012695	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs3012696	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs3012697	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs3012700	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs3012701	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs3012706	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs3012708	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs3012709	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs3012710	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs3012711	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs3012712	0.91[CEU][hapmap];0.88[CHB][hapmap]
rs3012713	0.88[CHB][hapmap]
rs41312820	0.94[EUR][1000 genomes]
rs474845	0.85[CEU][hapmap]
rs490961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs494348	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs506149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515913	0.82[JPT][hapmap]
rs527697	0.90[EUR][1000 genomes]
rs535305	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs535614	0.85[CEU][hapmap]
rs576347	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58010475	0.84[EUR][1000 genomes]
rs594370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs612198	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs617047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs617992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs619401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs625941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs636548	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs645583	0.86[EUR][1000 genomes]
rs646529	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs649990	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs656686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7025201	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs7025328	0.92[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap]
rs7035429	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs7044448	0.81[EUR][1000 genomes]
rs72699004	0.85[EUR][1000 genomes]
rs72699014	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72699023	0.87[EUR][1000 genomes]
rs72699031	0.83[ASN][1000 genomes]
rs72699039	0.81[EUR][1000 genomes]
rs7850660	0.88[CHB][hapmap]
rs7850999	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7855364	0.88[CHB][hapmap]
rs7861667	0.88[CHB][hapmap]
rs7861699	0.88[CHB][hapmap]
rs7866129	0.89[EUR][1000 genomes]
rs7871277	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1032529	chr9:3254763-3319778	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv539941	chr9:3254763-3319778	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
2	chr9:3223200-3277000	Weak transcription	HSMMtube	muscle
3	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
4	chr9:3224000-3275800	Weak transcription	Gastric	stomach
5	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
7	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:3238000-3276800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:3241400-3278000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:3241600-3276800	Weak transcription	Placenta	Placenta
11	chr9:3242000-3278000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:3242200-3287800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:3243800-3279200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:3245000-3275000	Weak transcription	HSMM	muscle
16	chr9:3245600-3277200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:3246800-3287000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:3250200-3276400	Weak transcription	HepG2	liver
19	chr9:3251600-3292600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:3252800-3278600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:3254200-3285600	Weak transcription	Fetal Heart	heart
22	chr9:3254800-3272000	Weak transcription	NH-A	brain
23	chr9:3255000-3293000	Weak transcription	Small Intestine	intestine
24	chr9:3255800-3292800	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:3256800-3293400	Weak transcription	Right Ventricle	heart
26	chr9:3257000-3289000	Weak transcription	Fetal Brain Male	brain
27	chr9:3257200-3274200	Weak transcription	Fetal Brain Female	brain
28	chr9:3257200-3275000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:3257200-3290200	Weak transcription	Brain Germinal Matrix	brain
30	chr9:3257200-3290200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:3257200-3290200	Weak transcription	Brain Substantia Nigra	brain
32	chr9:3257200-3294000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:3257200-3294400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:3257400-3279000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:3257400-3289000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr9:3257800-3285800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:3258000-3277400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:3260000-3276200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:3261400-3272600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr9:3261400-3281400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr9:3263000-3276200	Weak transcription	Fetal Kidney	kidney
42	chr9:3263000-3286800	Weak transcription	Liver	Liver
43	chr9:3263200-3275000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:3263200-3276200	Weak transcription	Fetal Stomach	stomach
45	chr9:3263200-3278400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:3263200-3294200	Weak transcription	Fetal Lung	lung
47	chr9:3263200-3294600	Weak transcription	Esophagus	oesophagus
48	chr9:3263200-3297800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr9:3263800-3286600	Weak transcription	Brain Hippocampus Middle	brain
50	chr9:3264000-3272200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links