Variant report

Variant	rs314310
Chromosome Location	chr7:100422169-100422170
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr7:100422162-100426238	IMR90	lung:	n/a	n/a
2	POLR2A	chr7:100422146-100422418	HepG2	liver:	n/a	n/a
3	SMC3	chr7:100422082-100425966	SK-N-SH	brain:	n/a	chr7:100425461-100425475 chr7:100425599-100425613 chr7:100423470-100423478 chr7:100423840-100423848 chr7:100423796-100423804
4	MXI1	chr7:100421736-100424014	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr7:100422030-100424812	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100421802..100424702-chr7:100482689..100484467,2	MCF-7	breast:
2	chr7:100417681..100419795-chr7:100419841..100422424,3	MCF-7	breast:
3	chr7:100422126..100425537-chr7:100471170..100475559,4	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:

Variant related genes	Relation type
RN7SL750P	TF binding region
SLC12A9	TF binding region
EPHB4	TF binding region
ENSG00000196411	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000263672	Chromatin interaction
ENSG00000087087	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs144173	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2230585	0.96[CEU][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247445	0.85[JPT][hapmap]
rs2250818	0.85[JPT][hapmap]
rs2406146	0.87[EUR][1000 genomes]
rs2472559	0.87[EUR][1000 genomes]
rs2571607	0.85[JPT][hapmap]
rs314309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs314319	0.89[ASN][1000 genomes]
rs314320	0.80[ASN][1000 genomes]
rs314322	0.80[ASN][1000 genomes]
rs314327	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs314341	0.81[EUR][1000 genomes]
rs314343	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs314344	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs314347	0.83[EUR][1000 genomes]
rs314353	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs314356	1.00[CEU][hapmap]
rs314357	0.91[EUR][1000 genomes]
rs314358	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs314359	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3847061	0.81[ASN][1000 genomes]
rs482308	0.83[CEU][hapmap]
rs489951	0.84[CEU][hapmap]
rs531503	0.84[CEU][hapmap]
rs539445	0.84[CEU][hapmap]
rs540330	0.84[CEU][hapmap]
rs542137	0.84[CEU][hapmap]

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	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
17	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer 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
18	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs314310	VGF	cis	cerebellum	SCAN
rs314310	MCM7	cis	cerebellum	SCAN

Chromatin state (count:92 , 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	chr7:100401600-100422600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:100401600-100423200	Weak transcription	Brain Anterior Caudate	brain
9	chr7:100401800-100422200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:100401800-100422200	Weak transcription	Fetal Heart	heart
11	chr7:100401800-100422400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:100401800-100422400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:100401800-100422400	Strong transcription	Fetal Intestine Large	intestine
14	chr7:100401800-100422600	Weak transcription	Fetal Brain Male	brain
15	chr7:100401800-100422600	Strong transcription	Fetal Intestine Small	intestine
16	chr7:100401800-100423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:100402000-100422600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:100402000-100422600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:100403400-100422400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:100408000-100422400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:100408200-100422400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:100411600-100423000	Weak transcription	Small Intestine	intestine
23	chr7:100411800-100422400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:100411800-100422400	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:100413200-100422600	Weak transcription	HSMM	muscle
26	chr7:100413400-100422600	Weak transcription	Hela-S3	cervix
27	chr7:100413600-100422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:100413600-100423400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr7:100414000-100422800	Weak transcription	Fetal Kidney	kidney
30	chr7:100415000-100422200	Strong transcription	Colon Smooth Muscle	Colon
31	chr7:100416400-100422200	Weak transcription	Fetal Brain Female	brain
32	chr7:100417400-100422400	Weak transcription	Stomach Mucosa	stomach
33	chr7:100419000-100422200	Strong transcription	Gastric	stomach
34	chr7:100419400-100422200	Strong transcription	A549	lung
35	chr7:100419600-100422200	Genic enhancers	Spleen	Spleen
36	chr7:100419800-100422400	Genic enhancers	Placenta	Placenta
37	chr7:100419800-100422400	Strong transcription	Rectal Smooth Muscle	rectum
38	chr7:100420000-100423200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:100420200-100422200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr7:100420400-100422400	Weak transcription	Right Atrium	heart
41	chr7:100420600-100422200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:100421200-100422200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:100421200-100422200	Weak transcription	NHDF-Ad	bronchial
44	chr7:100421200-100422400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:100421200-100422400	Genic enhancers	Pancreas	Pancrea
46	chr7:100421200-100422800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:100421400-100422200	Genic enhancers	Fetal Stomach	stomach
48	chr7:100421400-100422200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr7:100421400-100422200	Genic enhancers	Right Ventricle	heart
50	chr7:100421400-100422800	Weak transcription	Osteobl	bone

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