Variant report

Variant	rs6544167
Chromosome Location	chr2:38762291-38762292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38762163..38763872-chr2:38974751..38976812,2	K562	blood:
2	chr2:38760697..38762690-chr2:38978032..38979542,2	K562	blood:
3	chr2:38603492..38605404-chr2:38761964..38764089,2	K562	blood:
4	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
5	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
6	chr2:38602731..38605404-chr2:38761964..38763937,2	K562	blood:

Variant related genes	Relation type
ENSG00000119787	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2304005	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3213852	1.00[ASN][1000 genomes]
rs55957936	1.00[ASN][1000 genomes]
rs56251362	1.00[ASN][1000 genomes]
rs58441205	1.00[ASN][1000 genomes]
rs59114683	1.00[ASN][1000 genomes]
rs60695093	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6727765	1.00[ASN][1000 genomes]
rs6732384	0.85[AMR][1000 genomes]
rs6732743	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6755260	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72897608	1.00[ASN][1000 genomes]
rs72905837	1.00[ASN][1000 genomes]
rs72905847	1.00[ASN][1000 genomes]
rs72905860	1.00[ASN][1000 genomes]
rs72905861	1.00[ASN][1000 genomes]
rs72905863	1.00[ASN][1000 genomes]
rs72905868	1.00[ASN][1000 genomes]
rs72905869	1.00[ASN][1000 genomes]
rs72905871	1.00[ASN][1000 genomes]
rs72905899	1.00[ASN][1000 genomes]
rs73929050	0.82[ASN][1000 genomes]
rs73929059	0.85[AMR][1000 genomes]
rs73931077	0.85[AMR][1000 genomes]
rs73931606	0.85[AMR][1000 genomes]
rs7579589	0.85[AMR][1000 genomes]
rs7606435	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7606552	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9789532	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38751200-38762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:38755600-38762800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:38755600-38763000	Weak transcription	Esophagus	oesophagus
4	chr2:38755600-38763000	Weak transcription	Pancreas	Pancrea
5	chr2:38756000-38762800	Weak transcription	Right Atrium	heart
6	chr2:38756800-38762800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:38759600-38763000	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:38759600-38763000	Weak transcription	Brain Substantia Nigra	brain
9	chr2:38759800-38763000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:38760400-38763000	Enhancers	K562	blood
11	chr2:38760600-38763200	Weak transcription	Aorta	Aorta
12	chr2:38761000-38762400	Weak transcription	Adipose Nuclei	Adipose
13	chr2:38761000-38762400	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr2:38761000-38762600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:38761000-38762600	Bivalent Enhancer	HepG2	liver
16	chr2:38761000-38763800	Active TSS	Colon Smooth Muscle	Colon
17	chr2:38761400-38763000	Enhancers	Brain Anterior Caudate	brain
18	chr2:38761600-38762600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:38761600-38763000	Weak transcription	Primary B cells from cord blood	blood
20	chr2:38761600-38763000	Weak transcription	GM12878-XiMat	blood
21	chr2:38762000-38762400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:38762000-38763000	Bivalent Enhancer	Fetal Intestine Large	intestine
23	chr2:38762000-38763400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr2:38762200-38762400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:38762200-38762600	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:38762200-38762800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:38762200-38762800	Bivalent Enhancer	Placenta	Placenta
28	chr2:38762200-38762800	Active TSS	Rectal Smooth Muscle	rectum
29	chr2:38762200-38762800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:38762200-38763000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr2:38762200-38763400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr2:38762200-38763800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr2:38762200-38763800	Enhancers	Fetal Brain Male	brain

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