Variant report

Variant	rs28494902
Chromosome Location	chr7:6768519-6768520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr7:6768207-6768628	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6745463..6748475-chr7:6767656..6769994,3	K562	blood:
2	chr7:6746161..6747688-chr7:6768318..6771249,2	MCF-7	breast:
3	chr7:6768428..6771621-chr7:6773707..6775724,3	MCF-7	breast:
4	chr7:6616941..6618678-chr7:6767339..6769412,2	MCF-7	breast:
5	chr7:6675529..6677980-chr7:6768487..6770695,2	K562	blood:
6	chr7:6744871..6747873-chr7:6767656..6771321,4	K562	blood:
7	chr7:6767588..6769922-chr7:6774691..6777140,2	MCF-7	breast:
8	chr7:6745224..6747442-chr7:6767898..6770902,3	MCF-7	breast:
9	chr7:6766860..6769459-chr7:6864426..6866111,2	MCF-7	breast:

No data

Variant related genes	Relation type
PMS2CL	TF binding region
ENSG00000136247	Chromatin interaction
ENSG00000164631	Chromatin interaction
ENSG00000205903	Chromatin interaction
ENSG00000146574	Chromatin interaction
ENSG00000187953	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10236353	0.81[ASN][1000 genomes]
rs10244591	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272921	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10441131	0.88[ASN][1000 genomes]
rs10951994	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12113879	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12534591	0.88[ASN][1000 genomes]
rs12535850	0.87[ASN][1000 genomes]
rs12536067	0.86[ASN][1000 genomes]
rs12536107	0.85[ASN][1000 genomes]
rs12537487	0.89[ASN][1000 genomes]
rs12539942	0.86[ASN][1000 genomes]
rs12540797	0.89[ASN][1000 genomes]
rs13236698	0.81[AMR][1000 genomes]
rs13247186	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462654	0.82[ASN][1000 genomes]
rs28649084	0.91[ASN][1000 genomes]
rs34857592	0.86[ASN][1000 genomes]
rs34899283	0.96[ASN][1000 genomes]
rs34947632	0.85[ASN][1000 genomes]
rs35121012	0.95[ASN][1000 genomes]
rs35291651	0.94[ASN][1000 genomes]
rs35644498	0.93[ASN][1000 genomes]
rs35768299	0.93[ASN][1000 genomes]
rs4724766	0.82[ASN][1000 genomes]
rs62439703	0.81[ASN][1000 genomes]
rs62439704	0.81[ASN][1000 genomes]
rs62439719	0.81[ASN][1000 genomes]
rs62439720	0.80[ASN][1000 genomes]
rs62439721	0.82[ASN][1000 genomes]
rs62439722	0.88[ASN][1000 genomes]
rs62439727	0.95[ASN][1000 genomes]
rs62439728	0.87[ASN][1000 genomes]
rs62439731	0.86[ASN][1000 genomes]
rs62439737	0.87[ASN][1000 genomes]
rs62439738	0.83[ASN][1000 genomes]
rs62439743	0.84[ASN][1000 genomes]
rs6463579	0.89[ASN][1000 genomes]
rs6463580	0.89[ASN][1000 genomes]
rs6954172	0.89[ASN][1000 genomes]
rs6975002	0.81[ASN][1000 genomes]
rs6979127	0.81[ASN][1000 genomes]
rs7779296	0.89[ASN][1000 genomes]
rs7784521	0.90[ASN][1000 genomes]
rs7789640	0.89[ASN][1000 genomes]
rs7792579	0.92[ASN][1000 genomes]
rs7792858	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7796846	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804542	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
4	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	17 gene(s)	inside rSNPs	diseases
5	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	esv1819001	chr7:6746810-6785602	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv966755	chr7:6750289-6769785	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv966754	chr7:6750289-6838266	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv887442	chr7:6753286-6820508	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887443	chr7:6753286-6832265	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887444	chr7:6753286-6855510	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887445	chr7:6758018-6843722	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv887446	chr7:6758018-6870635	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv887447	chr7:6764583-6843722	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv887448	chr7:6764583-6855510	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv887449	chr7:6764583-6870635	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	esv2757207	chr7:6764583-6977214	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
18	esv2759504	chr7:6764583-6977214	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 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	chr7:6747000-6768600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6754600-6768600	Weak transcription	Liver	Liver
3	chr7:6765000-6768600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr7:6765200-6768600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:6765200-6769000	Weak transcription	Spleen	Spleen
6	chr7:6765400-6768600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:6765800-6768600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:6765800-6768600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:6765800-6768600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:6766200-6768800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr7:6766200-6769000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:6766400-6768600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:6766400-6769000	Weak transcription	NHEK	skin
14	chr7:6766600-6768600	Weak transcription	Primary B cells from cord blood	blood
15	chr7:6766600-6768800	Weak transcription	Placenta	Placenta
16	chr7:6767600-6769000	Weak transcription	HSMMtube	muscle
17	chr7:6767600-6769000	Weak transcription	K562	blood
18	chr7:6768200-6770600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:6768400-6768600	Active TSS	Primary hematopoietic stem cells	blood
20	chr7:6768400-6768600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:6768400-6769200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:6768400-6769400	Flanking Active TSS	GM12878-XiMat	blood

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