Variant report

Variant	rs13257298
Chromosome Location	chr8:42764722-42764723
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	chr8:42748537..42752958-chr8:42763640..42765702,3	MCF-7	breast:
2	chr8:42750720..42756430-chr8:42762967..42765897,6	K562	blood:

Variant related genes	Relation type
ENSG00000266044	Chromatin interaction
ENSG00000168172	Chromatin interaction
ENSG00000120925	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1052654	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10958736	0.80[CEU][hapmap]
rs11984732	1.00[ASW][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs11986681	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11987893	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11990515	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11992567	0.91[LWK][hapmap]
rs11997799	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13248091	0.92[CEU][hapmap]
rs13251524	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13252221	0.92[CEU][hapmap]
rs13256221	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs13260731	0.92[CEU][hapmap]
rs13269584	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs13282019	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs1648121	0.81[CEU][hapmap]
rs16891663	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16891667	0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs17622577	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs17622732	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs2376493	0.81[ASW][hapmap]
rs34100417	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34143633	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs34152125	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs34210297	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs34242561	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs34489103	0.81[ASW][hapmap]
rs34864660	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35021392	0.82[EUR][1000 genomes]
rs35252795	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35390123	0.92[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs35688388	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36026629	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs57652067	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57797146	0.90[AFR][1000 genomes]
rs58729413	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60292433	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62515942	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62515949	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62517585	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6474429	0.81[CEU][hapmap]
rs67575305	0.82[EUR][1000 genomes]
rs6996034	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6999489	0.91[ASW][hapmap];0.85[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7004940	0.85[AFR][1000 genomes]
rs7014595	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71521600	0.82[EUR][1000 genomes]
rs71521601	0.82[AMR][1000 genomes]
rs7462864	0.89[AMR][1000 genomes]
rs773068	0.81[CEU][hapmap]
rs773069	0.81[CEU][hapmap]
rs7820326	0.85[YRI][hapmap]
rs7821062	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7829867	0.91[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7835435	0.81[CEU][hapmap]
rs7838845	0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034724	chr8:42386707-42772203	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
2	nsv890846	chr8:42625663-43240123	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
3	nsv1024688	chr8:42709414-43333639	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv539563	chr8:42709414-43333639	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv1033927	chr8:42748842-43575771	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv533812	chr8:42755447-43528350	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13257298	FNTA	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:42753600-42771000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:42753600-42771800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:42753600-42785800	Weak transcription	Esophagus	oesophagus
4	chr8:42754000-42768400	Weak transcription	Fetal Kidney	kidney
5	chr8:42754000-42769600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr8:42754000-42771000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr8:42754000-42771200	Weak transcription	Small Intestine	intestine
8	chr8:42754000-42771800	Weak transcription	Aorta	Aorta
9	chr8:42754000-42772000	Weak transcription	Colonic Mucosa	Colon
10	chr8:42754000-42814200	Weak transcription	Fetal Thymus	thymus
11	chr8:42754200-42764800	Weak transcription	NH-A	brain
12	chr8:42754200-42768000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:42754200-42771000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:42754200-42771400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:42754200-42775200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:42754400-42765200	Weak transcription	Osteobl	bone
17	chr8:42754400-42772000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:42754400-42806400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:42754600-42771600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr8:42754600-42772000	Weak transcription	Ovary	ovary
21	chr8:42754600-42781800	Weak transcription	Hela-S3	cervix
22	chr8:42754800-42812600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr8:42755000-42766200	Weak transcription	Fetal Stomach	stomach
24	chr8:42755000-42787600	Weak transcription	Fetal Brain Male	brain
25	chr8:42755400-42765600	Weak transcription	Fetal Lung	lung
26	chr8:42755400-42765800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr8:42755800-42764800	Weak transcription	Liver	Liver
28	chr8:42755800-42785800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr8:42756200-42765600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr8:42756200-42775000	Weak transcription	Right Ventricle	heart
31	chr8:42756200-42775200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr8:42756400-42768800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:42756400-42771000	Weak transcription	Left Ventricle	heart
34	chr8:42756400-42771200	Weak transcription	Right Atrium	heart
35	chr8:42756400-42771800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr8:42757200-42772000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr8:42757400-42765400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr8:42757400-42770400	Weak transcription	Psoas Muscle	Psoas
39	chr8:42757600-42767600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr8:42757600-42775000	Weak transcription	Fetal Heart	heart
41	chr8:42758200-42765600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr8:42758200-42771600	Weak transcription	Brain Hippocampus Middle	brain
43	chr8:42758200-42775400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr8:42758400-42766200	Weak transcription	Fetal Intestine Small	intestine
45	chr8:42758400-42768800	Weak transcription	Brain Substantia Nigra	brain
46	chr8:42758400-42769000	Weak transcription	Fetal Intestine Large	intestine
47	chr8:42758400-42771400	Weak transcription	Colon Smooth Muscle	Colon
48	chr8:42759400-42771000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr8:42759400-42771800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr8:42759800-42781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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