Variant report

Variant	rs28409739
Chromosome Location	chr7:26196902-26196903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:26190370..26193400-chr7:26195972..26200613,6	MCF-7	breast:
2	chr7:26187891..26202612-chr7:26221953..26234536,42	K562	blood:
3	chr7:26194381..26200740-chr7:26239082..26242871,5	K562	blood:
4	chr7:26189963..26195377-chr7:26195444..26205125,17	K562	blood:
5	chr7:26196217..26197790-chr7:26198735..26200576,2	K562	blood:
6	chr7:26187762..26202698-chr7:26218693..26233402,42	K562	blood:
7	chr7:26195498..26197303-chr7:26213085..26215858,2	MCF-7	breast:
8	chr7:26195366..26198244-chr7:26238444..26241052,4	MCF-7	breast:
9	chr7:26193972..26197065-chr7:26200401..26202395,4	MCF-7	breast:
10	chr7:26196259..26200156-chr7:26237694..26241726,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000273237	Chromatin interaction
ENSG00000050344	Chromatin interaction
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11971108	1.00[ASN][1000 genomes]
rs11971308	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971320	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971402	1.00[ASN][1000 genomes]
rs11972057	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974685	1.00[ASN][1000 genomes]
rs11975011	0.85[EUR][1000 genomes]
rs11977822	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980825	1.00[ASN][1000 genomes]
rs17321514	1.00[ASN][1000 genomes]
rs41275982	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754901	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813103	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56021640	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56132015	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56273868	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56276467	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56287413	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376224	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393994	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56413126	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57188228	1.00[ASN][1000 genomes]
rs57665417	1.00[ASN][1000 genomes]
rs59142558	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59344953	1.00[ASN][1000 genomes]
rs59371106	1.00[ASN][1000 genomes]
rs59685141	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59820708	1.00[ASN][1000 genomes]
rs60954252	1.00[ASN][1000 genomes]
rs61009175	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61405107	1.00[ASN][1000 genomes]
rs6948113	1.00[ASN][1000 genomes]
rs73279689	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73279692	1.00[ASN][1000 genomes]
rs73281517	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281521	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281523	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281527	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281529	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281530	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281532	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281538	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281546	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281548	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281550	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281551	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281554	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281562	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281563	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73281570	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793815	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7793849	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794205	1.00[ASN][1000 genomes]
rs7803860	1.00[ASN][1000 genomes]
rs7807030	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
2	nsv1019804	chr7:26057723-26214280	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv887849	chr7:26075094-26234302	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
5	nsv1034358	chr7:26142380-26219559	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1018971	chr7:26161228-26380361	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26192600-26197000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:26193400-26199400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr7:26193400-26200200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:26193600-26199800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:26194000-26197600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:26194000-26200400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr7:26194200-26200200	Enhancers	Fetal Thymus	thymus
8	chr7:26194600-26200000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:26195000-26197600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr7:26195200-26197000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:26195200-26197000	Flanking Active TSS	NHEK	skin
12	chr7:26195800-26197600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:26195800-26197800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:26195800-26198200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:26195800-26198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:26195800-26198800	Enhancers	Placenta	Placenta
17	chr7:26195800-26199000	Weak transcription	Esophagus	oesophagus
18	chr7:26195800-26200800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr7:26195800-26201000	Weak transcription	Psoas Muscle	Psoas
20	chr7:26196000-26197000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr7:26196000-26197800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr7:26196000-26198200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:26196000-26200800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr7:26196000-26200800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr7:26196000-26201400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr7:26196200-26197000	Enhancers	Dnd41	blood
27	chr7:26196200-26197600	Enhancers	Primary T cells from cord blood	blood
28	chr7:26196200-26200400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:26196400-26197200	Weak transcription	HepG2	liver
30	chr7:26196400-26197200	Enhancers	NH-A	brain
31	chr7:26196400-26197400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:26196400-26197400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr7:26196400-26198000	Weak transcription	Fetal Intestine Large	intestine
34	chr7:26196400-26198200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:26196400-26198200	Enhancers	Primary hematopoietic stem cells	blood
36	chr7:26196400-26198600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr7:26196400-26198600	Weak transcription	Fetal Kidney	kidney
38	chr7:26196400-26199200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:26196400-26200400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:26196400-26205800	Weak transcription	Gastric	stomach
41	chr7:26196600-26197000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:26196600-26197000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:26196600-26197000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr7:26196600-26197000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr7:26196600-26197200	Weak transcription	A549	lung
46	chr7:26196600-26197600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:26196600-26197800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:26196600-26198000	Weak transcription	Fetal Intestine Small	intestine
49	chr7:26196600-26198200	Weak transcription	Spleen	Spleen
50	chr7:26196600-26198200	Weak transcription	K562	blood

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