Variant report

Variant	rs12154641
Chromosome Location	chr7:77975624-77975625
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	KAP1	chr7:77974421-77975639	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
RPL13AP17	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10254017	0.80[ASN][1000 genomes]
rs12705409	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13233399	0.84[GIH][hapmap]
rs1860538	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1990370	0.84[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2075013	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2075014	0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2159511	0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs2534646	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2534647	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2534648	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2534649	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691513	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2691530	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2691532	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2691533	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691535	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2691538	0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2691539	0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2691540	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691544	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691545	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2691546	0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4371942	0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4374924	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4556031	0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6976483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798308	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs798309	0.95[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs798310	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs798314	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs798317	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv607654	chr7:77537964-78014329	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12154641	TNFRSF25	trans	parietal	SCAN
rs12154641	SRRM3	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:77946200-77976000	Weak transcription	Aorta	Aorta
2	chr7:77953600-77986600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:77957000-77975800	Weak transcription	Brain Angular Gyrus	brain
4	chr7:77957200-77975800	Weak transcription	Brain Substantia Nigra	brain
5	chr7:77957600-77976000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:77957600-77978600	Weak transcription	Brain Anterior Caudate	brain
7	chr7:77958000-77979800	Weak transcription	Fetal Brain Female	brain
8	chr7:77964000-77981800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:77970200-77978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:77970600-77978400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:77972600-77976200	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:77972800-78001200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:77973600-77977400	Enhancers	Fetal Heart	heart
14	chr7:77974000-77980000	Weak transcription	Pancreas	Pancrea
15	chr7:77974800-77976000	Enhancers	Fetal Intestine Small	intestine
16	chr7:77975000-77976000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr7:77975000-77978600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:77975200-77975800	Enhancers	Stomach Mucosa	stomach
19	chr7:77975400-77976200	Enhancers	Fetal Brain Male	brain
20	chr7:77975400-77976800	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:77975600-77976000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr7:77975600-77992000	Weak transcription	Ovary	ovary

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