Variant report

Variant	rs1738240
Chromosome Location	chr6:38763733-38763734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38762200..38765807-chr6:38769309..38772341,3	K562	blood:
2	chr6:38756316..38758833-chr6:38761826..38764671,2	MCF-7	breast:
3	chr6:38763015..38763945-chr6:38839605..38840402,3	MCF-7	breast:
4	chr6:38761644..38764833-chr6:38770187..38773339,3	K562	blood:
5	chr6:38763255..38763863-chr6:38901115..38901700,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1018437	0.93[JPT][hapmap]
rs1033525	0.83[ASN][1000 genomes]
rs1033526	0.83[ASN][1000 genomes]
rs1157884	0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1614699	0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1630487	0.92[ASN][1000 genomes]
rs1678638	0.88[CEU][hapmap];0.93[JPT][hapmap]
rs1678657	0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1678661	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs1678667	0.88[ASN][1000 genomes]
rs1678669	0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1678675	0.86[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs1678717	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1678718	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678725	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678727	0.87[ASN][1000 genomes]
rs1678742	0.93[JPT][hapmap]
rs1738177	0.88[CHB][hapmap]
rs1738184	0.88[CEU][hapmap];0.93[JPT][hapmap]
rs1738192	0.93[JPT][hapmap]
rs1738199	0.80[ASN][1000 genomes]
rs1738203	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1738231	0.81[JPT][hapmap]
rs1738232	0.95[ASN][1000 genomes]
rs1738236	0.95[ASN][1000 genomes]
rs1738238	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738239	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738241	0.88[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs1738243	0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1738247	0.85[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs1738263	0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2206860	0.88[CHB][hapmap]
rs2395709	0.93[JPT][hapmap]
rs4286777	1.00[JPT][hapmap]
rs4380739	0.86[JPT][hapmap]
rs4386804	0.93[JPT][hapmap]
rs4391252	0.93[JPT][hapmap]
rs4443498	0.93[JPT][hapmap]
rs4571559	0.93[JPT][hapmap]
rs4590258	0.93[JPT][hapmap]
rs4711558	0.93[JPT][hapmap]
rs4714193	0.93[JPT][hapmap]
rs6458080	0.93[JPT][hapmap]
rs6458081	0.93[JPT][hapmap]
rs6931736	0.93[JPT][hapmap]
rs761348	0.95[ASN][1000 genomes]
rs862422	0.88[CEU][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap]
rs862425	0.88[CEU][hapmap];0.93[JPT][hapmap]
rs862427	0.93[JPT][hapmap]
rs9296265	0.93[JPT][hapmap]
rs9357290	0.93[JPT][hapmap]
rs9366982	0.93[JPT][hapmap]
rs9369089	0.93[JPT][hapmap]
rs9380789	0.93[JPT][hapmap]
rs9380791	0.81[JPT][hapmap]
rs9380796	0.93[JPT][hapmap]
rs9380798	0.93[JPT][hapmap]
rs9380799	0.93[JPT][hapmap]
rs9394531	0.88[CHB][hapmap]
rs9394547	0.93[JPT][hapmap]
rs9394550	0.93[JPT][hapmap]
rs982705	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs984523	0.92[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv462916	chr6:38747770-38782401	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv602960	chr6:38747770-38782401	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1738240	ANKS1A	cis	parietal	SCAN
rs1738240	GLO1	cis	Esophagus Mucosa	GTEx
rs1738240	GUCA1B	cis	cerebellum	SCAN
rs1738240	MDFI	cis	parietal	SCAN
rs1738240	LRFN2	cis	cerebellum	SCAN
rs1738240	RPL7L1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38754600-38764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:38763200-38763800	Enhancers	K562	blood
3	chr6:38763400-38764000	Enhancers	HUVEC	blood vessel
4	chr6:38763400-38764200	Enhancers	Pancreas	Pancrea
5	chr6:38763400-38764200	Enhancers	HMEC	breast
6	chr6:38763400-38764400	Enhancers	NHEK	skin
7	chr6:38763400-38768600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:38763600-38763800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:38763600-38764400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:38763600-38765200	Enhancers	Fetal Kidney	kidney
11	chr6:38763600-38765400	Enhancers	Fetal Intestine Large	intestine
12	chr6:38763600-38765600	Enhancers	Stomach Mucosa	stomach
13	chr6:38763600-38766800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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