Variant report

Variant	rs12727947
Chromosome Location	chr1:212417130-212417131
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	RCOR1	chr1:212417062-212417206	K562	blood:	n/a	n/a
2	TAL1	chr1:212417038-212417203	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212416179..212418074-chr1:212422362..212425881,3	K562	blood:
2	chr1:212385419..212387445-chr1:212414285..212417488,3	K562	blood:
3	chr1:212414204..212417772-chr1:212418799..212421886,6	K562	blood:

Variant related genes	Relation type
ENSG00000226251	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10494951	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10863960	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863961	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863963	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11119899	0.98[ASN][1000 genomes]
rs11119919	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11119920	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11119924	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11119930	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11576437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11579999	0.88[ASN][1000 genomes]
rs11580285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11585215	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11587555	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11588867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11589817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590242	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs11590672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12060029	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12064553	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12066356	0.98[ASN][1000 genomes]
rs12096035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12722832	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726409	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12728266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12730098	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12743785	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12745269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12746203	1.00[AFR][1000 genomes]
rs12747025	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756678	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1470390	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1493600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1530451	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17721302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120770	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs2297306	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2358448	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2358454	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs34212128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34244392	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34447409	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34740542	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35872305	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55814152	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6661987	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6667199	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6676208	0.87[TSI][hapmap]
rs6693849	1.00[YRI][hapmap]
rs71646153	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7518399	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs7521041	0.98[ASN][1000 genomes]
rs7531219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs968531	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968532	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv997899	chr1:212416909-212417311	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12727947	RP11-15I11.3	cis	Nerve Tibial	GTEx
rs12727947	RP11-15I11.3	cis	lung	GTEx
rs12727947	RP11-15I11.3	cis	Thyroid	GTEx
rs12727947	KCNH1	cis	cerebellum	SCAN
rs12727947	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212412200-212417400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:212412200-212417400	Weak transcription	GM12878-XiMat	blood
3	chr1:212412400-212417800	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:212412400-212420600	Weak transcription	Fetal Lung	lung
5	chr1:212413200-212420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:212415200-212419800	Weak transcription	Spleen	Spleen
7	chr1:212415200-212420400	Weak transcription	Fetal Heart	heart
8	chr1:212415200-212420800	Weak transcription	Fetal Intestine Small	intestine
9	chr1:212415400-212417200	Enhancers	Stomach Mucosa	stomach
10	chr1:212416000-212417400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:212416000-212418200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:212416000-212420600	Weak transcription	Osteobl	bone
13	chr1:212416200-212417400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:212416200-212420600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:212416400-212420200	Weak transcription	HUVEC	blood vessel
16	chr1:212416400-212420600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:212416400-212420600	Weak transcription	Lung	lung
18	chr1:212416400-212420600	Enhancers	HepG2	liver
19	chr1:212416400-212421400	Weak transcription	Psoas Muscle	Psoas
20	chr1:212416600-212417400	Enhancers	K562	blood
21	chr1:212416600-212417800	Weak transcription	Fetal Intestine Large	intestine
22	chr1:212416600-212417800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:212416600-212420000	Weak transcription	Right Atrium	heart
24	chr1:212416600-212420200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:212416600-212420600	Weak transcription	Fetal Stomach	stomach
26	chr1:212416600-212420600	Weak transcription	Left Ventricle	heart
27	chr1:212416600-212420600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:212416600-212420600	Weak transcription	Right Ventricle	heart
29	chr1:212416600-212420600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:212416600-212420800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:212416600-212430000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:212416800-212417600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:212416800-212418000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:212416800-212420200	Weak transcription	Adipose Nuclei	Adipose
35	chr1:212416800-212420800	Weak transcription	Liver	Liver
36	chr1:212417000-212417400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:212417000-212419000	Enhancers	Monocytes-CD14+_RO01746	blood

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