Variant report

Variant	rs9457256
Chromosome Location	chr6:167436461-167436462
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	POLR2A	chr6:167436393-167436651	K562	blood:	n/a	n/a
2	POLR2A	chr6:167436284-167438279	K562	blood:	n/a	n/a
3	POLR2A	chr6:167436320-167436587	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:167436331-167436640	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr6:167436395-167436765	HL-60	blood:	n/a	n/a
6	POLR2A	chr6:167436394-167436745	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:167436296-167436959	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:167436413-167436596	Gliobla	brain:	n/a	n/a
9	CTCF	chr6:167436460-167436610	RPTEC	kidney:	n/a	n/a
10	POLR2A	chr6:167436367-167437331	K562	blood:	n/a	n/a

Variant related genes	Relation type
FGFR1OP	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10455982	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10484530	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10484531	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10946203	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946205	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10946207	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946208	0.87[AMR][1000 genomes]
rs12208359	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12209395	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212247	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12213683	0.82[AMR][1000 genomes]
rs12526548	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12528323	0.82[AMR][1000 genomes]
rs12528689	0.82[AMR][1000 genomes]
rs12529876	0.82[AMR][1000 genomes]
rs13195812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13204839	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13208636	0.82[AMR][1000 genomes]
rs1322077	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17524252	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1794696	0.89[ASN][1000 genomes]
rs1811120	0.81[ASN][1000 genomes]
rs1894603	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2001114	0.85[AMR][1000 genomes]
rs2038580	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2181059	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2237272	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237273	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237274	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2237276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237277	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2239826	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2239827	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2282860	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2282861	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2285148	0.82[AMR][1000 genomes]
rs2301436	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239933	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs239935	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2757042	0.81[ASN][1000 genomes]
rs2769352	0.83[ASN][1000 genomes]
rs35171809	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs364451	0.81[ASN][1000 genomes]
rs3752520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398278	0.84[ASN][1000 genomes]
rs404222	0.89[ASN][1000 genomes]
rs408080	0.86[ASN][1000 genomes]
rs427824	0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs444988	0.83[ASN][1000 genomes]
rs4710171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4710175	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4710176	0.82[AMR][1000 genomes]
rs4710185	0.81[CHB][hapmap]
rs62436765	0.86[AMR][1000 genomes]
rs6456143	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6456146	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6456149	0.82[AMR][1000 genomes]
rs6456152	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6900701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6909180	0.82[AMR][1000 genomes]
rs6920858	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6921588	0.81[AMR][1000 genomes]
rs6923582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6929466	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7749278	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7766242	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs916331	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295384	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9295385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348211	0.83[ASN][1000 genomes]
rs9457249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9457251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9457252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9457254	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9457257	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9457258	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9457259	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9457260	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9459835	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9459836	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9459838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9459839	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9459840	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9459841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9459842	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9459845	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9459846	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9459849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9459854	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9459855	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9459872	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv464140	chr6:167426681-167492552	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9457256	AL133458.1	cis	lung	GTEx
rs9457256	RNASET2	cis	Whole Blood	GTEx
rs9457256	AL133458.1	cis	Whole Blood	GTEx
rs9457256	RNASET2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167413600-167438800	Weak transcription	Right Ventricle	heart
2	chr6:167413600-167449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:167413600-167452400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:167413800-167436800	Weak transcription	HSMMtube	muscle
5	chr6:167414600-167440800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:167414600-167441000	Weak transcription	Psoas Muscle	Psoas
7	chr6:167414600-167448000	Weak transcription	Small Intestine	intestine
8	chr6:167414600-167450200	Weak transcription	Stomach Mucosa	stomach
9	chr6:167415200-167440800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:167415400-167454000	Strong transcription	Fetal Thymus	thymus
11	chr6:167415400-167456600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:167416000-167444600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:167416200-167437400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:167417200-167455400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:167417600-167443000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:167417600-167446000	Strong transcription	Dnd41	blood
17	chr6:167417600-167454800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:167417800-167455200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:167419600-167439000	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:167419600-167440000	Weak transcription	Fetal Heart	heart
21	chr6:167420800-167447600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:167423000-167446400	Strong transcription	HepG2	liver
23	chr6:167423000-167457600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:167423400-167446400	Strong transcription	Liver	Liver
25	chr6:167423400-167452200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr6:167424000-167442600	Strong transcription	K562	blood
27	chr6:167424800-167442000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:167425600-167439800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:167425600-167441000	Weak transcription	NHLF	lung
30	chr6:167425600-167453000	Weak transcription	Brain Substantia Nigra	brain
31	chr6:167426600-167440200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:167426600-167450600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:167426800-167436800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:167426800-167438800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr6:167427000-167438800	Weak transcription	NHDF-Ad	bronchial
36	chr6:167427200-167436800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:167427200-167438200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:167427200-167438200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:167427200-167438800	Weak transcription	Brain Angular Gyrus	brain
40	chr6:167427200-167440000	Weak transcription	A549	lung
41	chr6:167429000-167438200	Weak transcription	NH-A	brain
42	chr6:167429000-167440200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:167429000-167440200	Weak transcription	Esophagus	oesophagus
44	chr6:167429200-167436600	Weak transcription	Fetal Brain Male	brain
45	chr6:167429200-167436800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:167429200-167437200	Weak transcription	Lung	lung
47	chr6:167429200-167437400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr6:167429200-167438200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:167429200-167438600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:167429200-167438800	Weak transcription	Brain Hippocampus Middle	brain

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