Variant report

Variant	rs41280998
Chromosome Location	chr7:100421665-100421666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100421658-100421796	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:100421364-100421937	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100419521..100422114-chr7:100465027..100466643,2	MCF-7	breast:
2	chr7:100411612..100416367-chr7:100416758..100421985,7	MCF-7	breast:
3	chr7:100417681..100419795-chr7:100419841..100422424,3	MCF-7	breast:
4	chr7:100271082..100273257-chr7:100420058..100422444,2	MCF-7	breast:
5	chr7:100403718..100405403-chr7:100421041..100423553,2	MCF-7	breast:

No data

Variant related genes	Relation type
EPHB4	TF binding region
SLC12A9	TF binding region
RN7SL750P	TF binding region
ENSG00000172354	Chromatin interaction
ENSG00000087077	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000263672	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs191137	0.85[EUR][1000 genomes]
rs28373056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314303	0.83[EUR][1000 genomes]
rs314308	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314333	0.83[EUR][1000 genomes]
rs3847060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847061	0.92[EUR][1000 genomes]
rs3847062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55982265	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56135824	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56173078	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326327	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59735023	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60720150	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73170798	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170800	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73172604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73172605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73172610	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
12	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
13	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv967435	chr7:100406273-100422961	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
15	nsv888800	chr7:100411278-100436446	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100399600-100422200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:100399600-100422200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:100399800-100422400	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr7:100399800-100422400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:100400000-100422200	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:100400400-100422200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:100401600-100421800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:100401600-100421800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:100401600-100422000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr7:100401600-100422000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:100401600-100422600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:100401600-100423200	Weak transcription	Brain Anterior Caudate	brain
13	chr7:100401800-100422200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:100401800-100422200	Weak transcription	Fetal Heart	heart
15	chr7:100401800-100422400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:100401800-100422400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:100401800-100422400	Strong transcription	Fetal Intestine Large	intestine
18	chr7:100401800-100422600	Weak transcription	Fetal Brain Male	brain
19	chr7:100401800-100422600	Strong transcription	Fetal Intestine Small	intestine
20	chr7:100401800-100423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:100402000-100421800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr7:100402000-100421800	Strong transcription	NHEK	skin
23	chr7:100402000-100422000	Strong transcription	Fetal Muscle Leg	muscle
24	chr7:100402000-100422600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:100402000-100422600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:100402200-100421800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:100402400-100422000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:100402400-100422000	Strong transcription	Fetal Lung	lung
29	chr7:100402600-100421800	Strong transcription	Lung	lung
30	chr7:100403200-100422000	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr7:100403400-100422400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:100403600-100421800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:100407400-100421800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:100408000-100422400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr7:100408200-100422400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:100408800-100421800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:100409000-100422000	Strong transcription	Left Ventricle	heart
38	chr7:100409000-100422000	Strong transcription	NHLF	lung
39	chr7:100411600-100423000	Weak transcription	Small Intestine	intestine
40	chr7:100411800-100422400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:100411800-100422400	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:100412000-100422000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:100413200-100422600	Weak transcription	HSMM	muscle
44	chr7:100413400-100422600	Weak transcription	Hela-S3	cervix
45	chr7:100413600-100421800	Strong transcription	Esophagus	oesophagus
46	chr7:100413600-100422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:100413600-100423400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:100414000-100422800	Weak transcription	Fetal Kidney	kidney
49	chr7:100415000-100422200	Strong transcription	Colon Smooth Muscle	Colon
50	chr7:100415800-100422000	Strong transcription	Muscle Satellite Cultured Cells	--

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