Variant report

Variant	rs1990954
Chromosome Location	chr5:126754165-126754166
allele	A/G
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	STAT3	chr5:126753990-126754252	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126753682..126756531-chr5:126759834..126762249,2	MCF-7	breast:

Variant related genes	Relation type
MEGF10	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10491250	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10519935	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10519949	1.00[MEX][hapmap]
rs11241930	1.00[CEU][hapmap]
rs11745840	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs12109001	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12654455	1.00[MEX][hapmap]
rs1363384	0.93[ASN][1000 genomes]
rs1363386	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1501993	0.93[ASN][1000 genomes]
rs1529468	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17164854	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17164922	1.00[CEU][hapmap]
rs17164923	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs17164951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17164957	1.00[CEU][hapmap]
rs17165013	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17165018	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17165019	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17684525	1.00[MEX][hapmap]
rs17684644	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17684655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17684679	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17684691	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17684740	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs17684775	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17685202	1.00[CEU][hapmap]
rs17763126	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17763172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1990955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042941	0.93[ASN][1000 genomes]
rs2042942	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2042943	0.93[ASN][1000 genomes]
rs2270933	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs3851468	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41298316	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157640	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60681812	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60998265	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595773	1.00[CEU][hapmap]
rs6865700	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6866275	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6873921	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874260	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877383	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6883445	1.00[CEU][hapmap]
rs6897163	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs73346906	0.87[ASN][1000 genomes]
rs73348744	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715710	0.93[ASN][1000 genomes]
rs7737871	1.00[CEU][hapmap];0.92[GIH][hapmap]
rs929781	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126742800-126760200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:126742800-126762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:126743000-126755600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:126743400-126760000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:126746200-126754800	Weak transcription	Psoas Muscle	Psoas
9	chr5:126746200-126758000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:126746400-126760800	Weak transcription	HSMM	muscle
11	chr5:126747000-126755000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:126747000-126759200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:126747200-126755000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:126748400-126755000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:126748400-126758600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:126749400-126755000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:126750200-126754200	Weak transcription	Brain Germinal Matrix	brain
18	chr5:126752200-126755200	Enhancers	Brain Cingulate Gyrus	brain
19	chr5:126752200-126756200	Enhancers	Brain Hippocampus Middle	brain
20	chr5:126752200-126756200	Enhancers	Brain Substantia Nigra	brain
21	chr5:126752400-126754800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr5:126752400-126755000	Enhancers	Brain Anterior Caudate	brain
23	chr5:126752800-126755400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr5:126752800-126755800	Enhancers	Brain Angular Gyrus	brain
25	chr5:126753200-126757400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:126753400-126754600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:126753400-126754800	Weak transcription	Fetal Brain Male	brain
28	chr5:126753400-126755200	Weak transcription	HSMMtube	muscle
29	chr5:126753400-126755600	Enhancers	Fetal Brain Female	brain
30	chr5:126753400-126761000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:126753600-126754800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:126753600-126754800	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:126753600-126754800	Weak transcription	Right Atrium	heart
34	chr5:126754000-126754200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:126754000-126754400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:126754000-126754800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links