Variant report

Variant	rs62440294
Chromosome Location	chr7:3339728-3339729
allele	A/G
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	CTCF	chr7:3339276-3341235	SK-N-SH	brain:	n/a	chr7:3339295-3339303 chr7:3340483-3340496 chr7:3339382-3339390
2	SMC3	chr7:3339220-3341228	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr7:3339463-3341267	SK-N-SH	brain:	n/a	n/a
4	CHD2	chr7:3339627-3339800	HepG2	liver:	n/a	n/a
5	RAD21	chr7:3339138-3341287	SK-N-SH	brain:	n/a	chr7:3339313-3339327 chr7:3339322-3339335
6	ZNF263	chr7:3339425-3341047	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3339718..3341766-chr7:3458306..3459954,2	K562	blood:
2	chr7:3254030..3256348-chr7:3338235..3340171,2	MCF-7	breast:

Variant related genes	Relation type
SDK1	TF binding region
ENSG00000211544	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11766873	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11770645	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11983024	0.91[ASN][1000 genomes]
rs12234397	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12700775	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700776	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700777	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12700780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17133257	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2334058	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34368704	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34469526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35888267	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36089007	0.88[ASN][1000 genomes]
rs36094267	0.92[EUR][1000 genomes]
rs4348387	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62437660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62437661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62437662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62437663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62437664	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62440295	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62441387	0.92[EUR][1000 genomes]
rs72576953	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72576955	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72576957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1803572	chr7:3327994-3341589	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv605885	chr7:3337081-3340551	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv16714	chr7:3339551-3340091	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv19885	chr7:3339551-3341631	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv3328363	chr7:3339726-3342349	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3335000-3340000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:3337600-3339800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:3338600-3340200	Enhancers	NHDF-Ad	bronchial
4	chr7:3339000-3339800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:3339200-3339800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:3339200-3339800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:3339200-3340000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr7:3339400-3339800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr7:3339400-3339800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:3339400-3339800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr7:3339400-3339800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:3339400-3339800	Bivalent Enhancer	Brain Germinal Matrix	brain
13	chr7:3339400-3340000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:3339400-3340000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
15	chr7:3339400-3340200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr7:3339400-3340200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:3339400-3340200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:3339400-3340200	Bivalent Enhancer	Fetal Thymus	thymus
19	chr7:3339400-3340600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr7:3339400-3340600	Bivalent Enhancer	Placenta	Placenta
21	chr7:3339600-3339800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
22	chr7:3339600-3339800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:3339600-3339800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
24	chr7:3339600-3339800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
25	chr7:3339600-3339800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
26	chr7:3339600-3339800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:3339600-3339800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:3339600-3339800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:3339600-3339800	Enhancers	Fetal Heart	heart
30	chr7:3339600-3339800	Enhancers	Pancreas	Pancrea
31	chr7:3339600-3339800	Enhancers	Right Ventricle	heart
32	chr7:3339600-3340000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr7:3339600-3340000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr7:3339600-3340000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr7:3339600-3340000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr7:3339600-3340000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
37	chr7:3339600-3340000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
38	chr7:3339600-3340000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:3339600-3340000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
40	chr7:3339600-3340000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:3339600-3340000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:3339600-3340000	Bivalent Enhancer	Adipose Nuclei	Adipose
43	chr7:3339600-3340000	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr7:3339600-3340000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr7:3339600-3340000	Flanking Bivalent TSS/Enh	HepG2	liver
46	chr7:3339600-3340200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
47	chr7:3339600-3340200	Bivalent Enhancer	Fetal Stomach	stomach
48	chr7:3339600-3340200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr7:3339600-3342600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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