Variant report

Variant	rs6746820
Chromosome Location	chr2:39370221-39370222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39357363..39365432-chr2:39365480..39370907,10	K562	blood:
2	chr2:39347290..39349608-chr2:39369956..39371650,2	MCF-7	breast:
3	chr2:39347197..39349488-chr2:39369964..39372941,3	K562	blood:
4	chr2:39370108..39372650-chr2:39376840..39380472,4	K562	blood:
5	chr2:39367193..39370444-chr2:39377653..39381134,4	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11888511	0.83[EUR][1000 genomes]
rs11898025	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023405	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17023552	0.83[EUR][1000 genomes]
rs17023573	0.83[EUR][1000 genomes]
rs17023584	0.83[EUR][1000 genomes]
rs2708227	1.00[AMR][1000 genomes]
rs3770661	0.83[EUR][1000 genomes]
rs56024079	0.83[EUR][1000 genomes]
rs56361338	0.83[EUR][1000 genomes]
rs57271382	0.83[EUR][1000 genomes]
rs57401773	0.83[EUR][1000 genomes]
rs59121834	0.83[EUR][1000 genomes]
rs59707152	0.83[EUR][1000 genomes]
rs61257289	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138484	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6544201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544206	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544207	1.00[ASN][1000 genomes]
rs6706379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718000	0.83[EUR][1000 genomes]
rs6731330	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72921023	0.83[EUR][1000 genomes]
rs72925446	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72927494	0.83[EUR][1000 genomes]
rs73923836	0.83[EUR][1000 genomes]
rs73923842	0.83[EUR][1000 genomes]
rs73923844	0.83[EUR][1000 genomes]
rs73923847	0.83[EUR][1000 genomes]
rs73924815	0.83[EUR][1000 genomes]
rs73924816	0.83[EUR][1000 genomes]
rs73924817	0.83[EUR][1000 genomes]
rs73930526	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73930538	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569943	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7589576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595102	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39363600-39371400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:39366800-39371200	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:39366800-39372400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:39367000-39370800	Enhancers	Primary B cells from cord blood	blood
5	chr2:39367800-39370800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr2:39368400-39371400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:39368600-39371200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:39368800-39377200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:39369200-39370400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:39369400-39370600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:39369400-39370600	Weak transcription	GM12878-XiMat	blood
12	chr2:39369400-39370800	Weak transcription	Adipose Nuclei	Adipose
13	chr2:39369400-39371800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:39369400-39373200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:39369600-39371000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:39369600-39371800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:39369600-39373200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:39369600-39380800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:39369800-39370400	Enhancers	K562	blood
20	chr2:39370000-39370400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:39370200-39371000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:39370200-39371400	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links