Variant report

Variant	rs28566958
Chromosome Location	chr7:97850822-97850823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97846624..97850033-chr7:97850682..97852457,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205356	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10249366	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10953247	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11761574	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11771397	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11771953	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772438	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11773779	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11984183	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533016	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12539676	0.88[EUR][1000 genomes]
rs12669622	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12704981	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270600	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270604	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394827	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28662014	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4727388	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727390	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729421	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56098787	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61575270	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62479836	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62479838	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6951479	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747631	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747632	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7787309	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs954050	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv888762	chr7:97829492-97853184	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv888763	chr7:97829492-97866291	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv888765	chr7:97834386-97853184	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv1812914	chr7:97846435-97860164	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv1849580	chr7:97846435-97860164	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28566958	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs28566958	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97823000-97851000	Weak transcription	HSMMtube	muscle
2	chr7:97825200-97851000	Weak transcription	Fetal Lung	lung
3	chr7:97836000-97851000	Weak transcription	NHLF	lung
4	chr7:97836800-97857200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:97839200-97851000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:97840200-97851000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:97840400-97852800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:97841000-97858600	Weak transcription	Psoas Muscle	Psoas
9	chr7:97841200-97852200	Weak transcription	A549	lung
10	chr7:97841200-97867800	Weak transcription	HUVEC	blood vessel
11	chr7:97841200-97880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:97841400-97858600	Weak transcription	NH-A	brain
13	chr7:97841400-97866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:97841400-97879400	Weak transcription	Fetal Brain Male	brain
15	chr7:97841400-97880200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:97841600-97851000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:97841600-97853800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:97841800-97867400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:97842200-97868400	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:97843400-97855000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:97843800-97857000	Weak transcription	Right Atrium	heart
22	chr7:97845200-97877400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:97845800-97851000	Weak transcription	Fetal Intestine Large	intestine
24	chr7:97846800-97856400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:97847000-97851000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:97847000-97851000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:97847000-97851200	Weak transcription	Small Intestine	intestine
28	chr7:97847200-97851000	Weak transcription	Left Ventricle	heart
29	chr7:97847400-97851000	Weak transcription	Aorta	Aorta
30	chr7:97847400-97851000	Weak transcription	Placenta	Placenta
31	chr7:97847400-97851000	Weak transcription	Dnd41	blood
32	chr7:97847600-97851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:97847600-97851000	Weak transcription	Colonic Mucosa	Colon
34	chr7:97847600-97851000	Weak transcription	Esophagus	oesophagus
35	chr7:97847600-97851000	Weak transcription	Gastric	stomach
36	chr7:97847600-97851000	Weak transcription	Right Ventricle	heart
37	chr7:97847600-97851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:97847800-97851000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:97847800-97851000	Weak transcription	Fetal Thymus	thymus
40	chr7:97847800-97851000	Weak transcription	Pancreas	Pancrea
41	chr7:97848000-97851000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:97848000-97851000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:97848000-97851000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr7:97848000-97851000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:97848000-97851000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:97848000-97852800	Weak transcription	HepG2	liver
47	chr7:97848000-97857600	Weak transcription	Stomach Mucosa	stomach
48	chr7:97848000-97877600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr7:97848000-97880600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:97848400-97851000	Weak transcription	Brain Hippocampus Middle	brain

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