Variant report

Variant	rs314311
Chromosome Location	chr7:100422481-100422482
allele	A/C
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	RAD21	chr7:100422224-100424797	SK-N-SH	brain:	n/a	chr7:100423965-100423978
2	MXI1	chr7:100422162-100426238	IMR90	lung:	n/a	n/a
3	POLR2A	chr7:100422235-100427552	HUVEC	blood vessel:	n/a	n/a
4	SIN3AK20	chr7:100422470-100426001	MCF-7	breast:	n/a	n/a
5	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
6	MXI1	chr7:100421736-100424014	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:100422030-100424812	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr7:100422476-100422492	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100421802..100424702-chr7:100482689..100484467,2	MCF-7	breast:
2	chr7:100026028..100027729-chr7:100422435..100425262,2	MCF-7	breast:
3	chr7:100422126..100425537-chr7:100471170..100475559,4	MCF-7	breast:
4	chr7:100410343..100413835-chr7:100422249..100426210,7	MCF-7	breast:
5	chr7:100403718..100405403-chr7:100421041..100423553,2	MCF-7	breast:

Variant related genes	Relation type
SLC12A9	TF binding region
RN7SL750P	TF binding region
EPHB4	TF binding region
ENSG00000078487	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12667888	1.00[CHB][hapmap]
rs12705092	1.00[CHB][hapmap]
rs160602	0.82[ASN][1000 genomes]
rs17884589	1.00[CHB][hapmap]
rs221005	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs221805	0.82[ASN][1000 genomes]
rs314296	0.82[ASN][1000 genomes]
rs314300	0.82[ASN][1000 genomes]
rs314304	0.82[ASN][1000 genomes]
rs314306	0.82[ASN][1000 genomes]
rs314307	0.83[ASN][1000 genomes]
rs314308	1.00[CHB][hapmap]
rs314312	0.94[ASN][1000 genomes]
rs314313	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs314314	0.83[ASN][1000 genomes]
rs314316	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs314317	0.83[ASN][1000 genomes]
rs314318	0.83[ASN][1000 genomes]
rs314337	0.88[ASN][1000 genomes]
rs314342	0.88[ASN][1000 genomes]
rs314345	0.88[ASN][1000 genomes]
rs314346	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs314354	0.88[ASN][1000 genomes]
rs314360	0.83[ASN][1000 genomes]
rs314361	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs314363	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs314364	0.88[ASN][1000 genomes]
rs314365	0.88[ASN][1000 genomes]
rs314366	0.88[ASN][1000 genomes]
rs314370	1.00[CHB][hapmap]
rs314373	1.00[CHB][hapmap]
rs3757868	1.00[CHB][hapmap]
rs6706	1.00[CHB][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs314311	ZNF3	cis	parietal	SCAN
rs314311	TRIM4	cis	cerebellum	SCAN
rs314311	C7orf59	cis	parietal	SCAN
rs314311	MCM7	cis	cerebellum	SCAN
rs314311	SRRT	cis	cerebellum	SCAN
rs314311	RELN	cis	parietal	SCAN
rs314311	ACHE	cis	Artery Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100401600-100422600	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr7:100401600-100423200	Weak transcription	Brain Anterior Caudate	brain
3	chr7:100401800-100422600	Weak transcription	Fetal Brain Male	brain
4	chr7:100401800-100422600	Strong transcription	Fetal Intestine Small	intestine
5	chr7:100401800-100423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:100402000-100422600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:100402000-100422600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:100411600-100423000	Weak transcription	Small Intestine	intestine
9	chr7:100413200-100422600	Weak transcription	HSMM	muscle
10	chr7:100413400-100422600	Weak transcription	Hela-S3	cervix
11	chr7:100413600-100423400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:100414000-100422800	Weak transcription	Fetal Kidney	kidney
13	chr7:100420000-100423200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:100421200-100422800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:100421400-100422800	Weak transcription	Osteobl	bone
16	chr7:100421400-100423000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:100421400-100423200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:100421600-100422800	Enhancers	Liver	Liver
19	chr7:100421800-100422600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:100421800-100422600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:100421800-100422600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:100421800-100422600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:100421800-100422600	Weak transcription	HSMMtube	muscle
24	chr7:100421800-100422800	Weak transcription	Esophagus	oesophagus
25	chr7:100421800-100423000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:100421800-100423000	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
27	chr7:100421800-100423400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:100421800-100424000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:100421800-100425000	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr7:100422000-100422600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:100422000-100422600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:100422000-100422600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:100422000-100422600	Transcr. at gene 5' and 3'	NHLF	lung
34	chr7:100422000-100422800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:100422000-100422800	Genic enhancers	K562	blood
36	chr7:100422000-100423000	Genic enhancers	Fetal Lung	lung
37	chr7:100422000-100423600	Flanking Active TSS	HUVEC	blood vessel
38	chr7:100422200-100422600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:100422200-100422600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:100422200-100422600	Genic enhancers	Colon Smooth Muscle	Colon
41	chr7:100422200-100422600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr7:100422200-100422800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:100422200-100422800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr7:100422200-100422800	Enhancers	NHDF-Ad	bronchial
45	chr7:100422200-100423000	Active TSS	Fetal Brain Female	brain
46	chr7:100422200-100423000	Flanking Active TSS	HMEC	breast
47	chr7:100422200-100423200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
48	chr7:100422200-100423200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
49	chr7:100422200-100423200	Enhancers	Fetal Heart	heart
50	chr7:100422200-100423400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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