Variant report

Variant	rs3181235
Chromosome Location	chr6:24655122-24655123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:
2	chr6:24653409..24658053-chr6:24717441..24721188,4	MCF-7	breast:
3	chr6:24653780..24658008-chr6:24658421..24664116,7	MCF-7	breast:
4	chr6:24652247..24658784-chr6:24665384..24668018,7	MCF-7	breast:
5	chr6:24653989..24657091-chr6:24719747..24721924,3	MCF-7	breast:
6	chr6:24650977..24653487-chr6:24654406..24656645,3	MCF-7	breast:
7	chr6:24654228..24658025-chr6:24716632..24719423,3	K562	blood:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000137261	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs16889592	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16901739	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249687	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883591	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2056998	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073013	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2294688	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294689	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294690	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328847	0.85[ASN][1000 genomes]
rs2876679	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3181230	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181233	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3181236	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3181237	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212229	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3212234	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7765052	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9358786	0.90[ASN][1000 genomes]
rs9358787	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366579	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9379679	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9379682	0.99[ASN][1000 genomes]
rs9393575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461050	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9467251	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467253	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9467257	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv883481	chr6:24652247-24659071	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24646400-24658800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:24646600-24655800	Weak transcription	Aorta	Aorta
3	chr6:24646800-24655600	Weak transcription	Pancreas	Pancrea
4	chr6:24646800-24662400	Weak transcription	Right Ventricle	heart
5	chr6:24646800-24662600	Weak transcription	Spleen	Spleen
6	chr6:24646800-24666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:24647000-24659000	Weak transcription	Stomach Mucosa	stomach
8	chr6:24647000-24662200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:24647000-24662400	Weak transcription	Lung	lung
10	chr6:24647000-24662600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:24647000-24666400	Weak transcription	Esophagus	oesophagus
12	chr6:24647200-24663400	Weak transcription	Fetal Kidney	kidney
13	chr6:24649400-24656600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:24649400-24659200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:24649400-24659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:24649400-24664800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:24649400-24665200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:24649800-24655600	Strong transcription	Fetal Thymus	thymus
19	chr6:24649800-24656200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:24650000-24657400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:24650000-24657400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:24650000-24658400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:24650000-24658400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr6:24650000-24658600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:24650000-24659000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:24650000-24663600	Strong transcription	Dnd41	blood
27	chr6:24650000-24665000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:24650200-24656000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr6:24650200-24656200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:24650200-24656600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:24650200-24657600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:24650200-24657600	Strong transcription	Placenta	Placenta
33	chr6:24650200-24658800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:24650200-24659000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:24650200-24659000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:24650200-24659000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:24650400-24655400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:24650400-24655600	Strong transcription	Hela-S3	cervix
39	chr6:24650400-24656200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:24650400-24656200	Strong transcription	Adipose Nuclei	Adipose
41	chr6:24650400-24656200	Strong transcription	Colon Smooth Muscle	Colon
42	chr6:24650400-24656200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:24650400-24656200	Strong transcription	GM12878-XiMat	blood
44	chr6:24650400-24658600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:24650600-24655600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:24650600-24656000	Strong transcription	Osteobl	bone
47	chr6:24650600-24658800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr6:24650800-24656000	Strong transcription	Fetal Muscle Leg	muscle
49	chr6:24651000-24659800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:24651200-24659200	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links