Variant report

Variant	rs10940644
Chromosome Location	chr5:58613660-58613661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1031197	1.00[JPT][hapmap]
rs10491352	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11954668	1.00[JPT][hapmap]
rs11959132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11959567	1.00[JPT][hapmap]
rs12189022	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12519611	0.81[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12521263	0.86[EUR][1000 genomes]
rs12522944	0.84[EUR][1000 genomes]
rs1445948	1.00[JPT][hapmap]
rs1445952	0.83[EUR][1000 genomes]
rs1445953	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1445954	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1579848	0.86[EUR][1000 genomes]
rs1579849	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889479	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16889499	0.82[EUR][1000 genomes]
rs16889518	0.83[EUR][1000 genomes]
rs17444185	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs17528522	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs17528578	0.83[EUR][1000 genomes]
rs17628114	1.00[JPT][hapmap]
rs17780175	1.00[JPT][hapmap]
rs1823070	0.82[EUR][1000 genomes]
rs1838733	1.00[JPT][hapmap]
rs1840846	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867711	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1867712	0.82[EUR][1000 genomes]
rs1947090	0.80[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1947095	0.82[EUR][1000 genomes]
rs2013979	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2014012	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2021775	1.00[JPT][hapmap]
rs2028836	0.80[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[JPT][hapmap]
rs4700325	1.00[JPT][hapmap]
rs4700328	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6858946	1.00[JPT][hapmap]
rs6877508	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6891161	1.00[JPT][hapmap]
rs7443333	0.84[EUR][1000 genomes]
rs7719441	1.00[JPT][hapmap]
rs889231	1.00[CHB][hapmap];0.90[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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2760953	chr5:58609468-58620440	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58607800-58616400	Enhancers	Fetal Heart	heart
2	chr5:58610000-58613800	Enhancers	Fetal Muscle Leg	muscle
3	chr5:58611200-58613800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr5:58612400-58613800	Enhancers	Psoas Muscle	Psoas
5	chr5:58612400-58614200	Enhancers	Fetal Kidney	kidney
6	chr5:58612400-58616200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:58612600-58613800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:58612600-58613800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:58612600-58613800	Enhancers	Fetal Intestine Large	intestine
10	chr5:58612600-58613800	Enhancers	Ovary	ovary
11	chr5:58612600-58614000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:58612600-58614000	Enhancers	Brain Anterior Caudate	brain
13	chr5:58612600-58614000	Enhancers	Brain Hippocampus Middle	brain
14	chr5:58612600-58614000	Enhancers	Fetal Stomach	stomach
15	chr5:58612600-58614200	Enhancers	Fetal Intestine Small	intestine
16	chr5:58612600-58614200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr5:58612600-58614600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:58612600-58615000	Enhancers	Fetal Lung	lung
19	chr5:58612800-58613800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr5:58612800-58613800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:58612800-58613800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr5:58612800-58613800	Enhancers	Duodenum Mucosa	Duodenum
23	chr5:58612800-58613800	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr5:58612800-58614000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:58612800-58614000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:58612800-58614000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:58612800-58614000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:58612800-58614000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:58612800-58614000	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr5:58612800-58614200	Enhancers	Adipose Nuclei	Adipose
31	chr5:58612800-58614200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr5:58612800-58614200	Enhancers	Brain Substantia Nigra	brain
33	chr5:58612800-58614400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr5:58612800-58614400	Enhancers	Stomach Mucosa	stomach
35	chr5:58612800-58616000	Enhancers	Brain Angular Gyrus	brain
36	chr5:58612800-58616600	Enhancers	A549	lung
37	chr5:58612800-58627200	Weak transcription	Aorta	Aorta
38	chr5:58613000-58613800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr5:58613000-58613800	Enhancers	Fetal Brain Female	brain
40	chr5:58613000-58614000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:58613000-58614000	Enhancers	NHEK	skin
42	chr5:58613000-58614200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:58613000-58614200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:58613000-58614200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr5:58613200-58614000	Enhancers	Brain Cingulate Gyrus	brain
46	chr5:58613200-58614200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:58613200-58615200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:58613400-58613800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:58613400-58613800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:58613400-58613800	Flanking Active TSS	Colon Smooth Muscle	Colon

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