Variant report

Variant	rs12907139
Chromosome Location	chr15:73521566-73521567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73518381..73521870-chr15:73524452..73526863,3	K562	blood:
2	chr15:73518381..73521603-chr15:73524397..73526863,3	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10048053	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1023924	0.80[JPT][hapmap]
rs10438294	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10467949	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11072406	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11072409	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1131854	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11632639	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs11633469	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636241	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11639213	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12050774	0.80[JPT][hapmap]
rs12050848	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12708506	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899246	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12902768	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916928	0.84[EUR][1000 genomes]
rs1479337	0.87[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1479339	0.82[CHB][hapmap]
rs1479340	0.88[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1564345	0.88[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs17762516	0.91[ASN][1000 genomes]
rs17762600	0.80[JPT][hapmap]
rs17829830	0.80[JPT][hapmap]
rs17829836	0.93[ASN][1000 genomes]
rs17829957	0.80[JPT][hapmap]
rs1871385	0.92[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2010793	0.82[ASN][1000 genomes]
rs2046017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2127277	0.88[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2194924	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2251205	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2415147	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899784	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs34013312	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35450875	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3736510	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3743489	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3784793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784796	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4132535	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs4381562	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4776630	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4777582	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs4777583	0.84[EUR][1000 genomes]
rs4777589	0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4777591	0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs56157337	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58060856	0.90[ASN][1000 genomes]
rs62017779	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495047	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7164894	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7169083	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs7172021	0.88[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7172396	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7175329	0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs747872	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs747873	0.89[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8024575	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026579	0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs8027588	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8029106	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035063	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035925	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8040516	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8042700	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs922516	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs9672588	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9806496	0.94[ASN][1000 genomes]
rs9920186	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs9972523	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
2	chr15:73493400-73528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:73497800-73541800	Weak transcription	Fetal Kidney	kidney
4	chr15:73509400-73525000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:73509600-73528800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:73516400-73523800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:73516400-73524000	Weak transcription	Fetal Brain Male	brain
8	chr15:73516600-73528200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:73516800-73528600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:73517600-73523800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:73517600-73528400	Weak transcription	Fetal Lung	lung
12	chr15:73517800-73521600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr15:73518000-73523800	Weak transcription	Gastric	stomach
14	chr15:73518200-73522800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:73518200-73528600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:73518200-73540800	Weak transcription	Colonic Mucosa	Colon
17	chr15:73518400-73531800	Weak transcription	Aorta	Aorta
18	chr15:73518600-73524800	Weak transcription	Lung	lung
19	chr15:73518600-73525000	Weak transcription	Brain Angular Gyrus	brain
20	chr15:73518600-73528600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:73518600-73528600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:73518600-73528800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:73518600-73529800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:73518600-73534000	Weak transcription	Right Ventricle	heart
25	chr15:73518800-73522600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:73518800-73523600	Weak transcription	Fetal Intestine Small	intestine
27	chr15:73518800-73523800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:73518800-73523800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:73518800-73524000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:73518800-73524000	Weak transcription	Fetal Stomach	stomach
31	chr15:73518800-73524800	Weak transcription	Fetal Intestine Large	intestine
32	chr15:73518800-73526400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:73518800-73546200	Weak transcription	Psoas Muscle	Psoas
34	chr15:73518800-73547800	Weak transcription	Left Ventricle	heart
35	chr15:73519000-73521800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:73519000-73523800	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:73519200-73524000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:73519400-73522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:73519400-73524000	Weak transcription	Osteobl	bone
40	chr15:73520000-73523800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:73520400-73524000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:73520400-73524000	Weak transcription	Brain Substantia Nigra	brain
43	chr15:73520400-73524000	Weak transcription	Stomach Mucosa	stomach
44	chr15:73520400-73528400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:73520400-73528600	Weak transcription	Brain Anterior Caudate	brain
46	chr15:73520400-73528600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:73520400-73562400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:73520600-73522000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:73520600-73523800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:73520600-73523800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links