Variant report

Variant	rs62437662
Chromosome Location	chr7:3340021-3340022
allele	C/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	POLR2A	chr7:3339859-3340135	MCF-7	breast:	n/a	n/a
2	CTCF	chr7:3339276-3341235	SK-N-SH	brain:	n/a	chr7:3339295-3339303 chr7:3340483-3340496 chr7:3339382-3339390
3	SIN3AK20	chr7:3339879-3341185	PANC-1	pancreas:	n/a	n/a
4	SMC3	chr7:3339220-3341228	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr7:3340000-3340150	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr7:3339844-3341257	MCF-7	breast:	n/a	n/a
7	MAX	chr7:3339896-3341192	HepG2	liver:	n/a	chr7:3340556-3340566
8	CTCF	chr7:3339980-3340130	GM12870	blood:	n/a	n/a
9	MXI1	chr7:3339463-3341267	SK-N-SH	brain:	n/a	n/a
10	BACH1	chr7:3339959-3340991	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr7:3339949-3341060	HepG2	liver:	n/a	chr7:3340556-3340566
12	MAX	chr7:3339823-3341087	MCF-7	breast:	n/a	chr7:3340556-3340566
13	MAX	chr7:3339893-3341102	HepG2	liver:	n/a	chr7:3340556-3340566
14	RAD21	chr7:3339138-3341287	SK-N-SH	brain:	n/a	chr7:3339313-3339327 chr7:3339322-3339335
15	POLR2A	chr7:3339755-3340209	SK-N-MC	brain:	n/a	n/a
16	ZNF263	chr7:3339425-3341047	HEK293-T-REx	kidney:	n/a	n/a
17	CTCF	chr7:3339900-3340050	GM12873	blood:	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: 46 )
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];0.95[ASN][1000 genomes]
rs11770645	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11983024	0.91[ASN][1000 genomes]
rs12234397	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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];1.00[ASN][1000 genomes]
rs12700777	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700779	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133257	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[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];0.87[ASN][1000 genomes]
rs34469526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35888267	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36089007	0.89[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];1.00[ASN][1000 genomes]
rs62437663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62437664	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62440295	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.91[ASN][1000 genomes]
rs72576955	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72576957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
17	esv3345863	chr7:3339851-3342399	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv1802865	chr7:3339987-3341589	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3338600-3340200	Enhancers	NHDF-Ad	bronchial
2	chr7:3339400-3340200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr7:3339400-3340200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:3339400-3340200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:3339400-3340200	Bivalent Enhancer	Fetal Thymus	thymus
6	chr7:3339400-3340600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr7:3339400-3340600	Bivalent Enhancer	Placenta	Placenta
8	chr7:3339600-3340200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr7:3339600-3340200	Bivalent Enhancer	Fetal Stomach	stomach
10	chr7:3339600-3340200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
11	chr7:3339600-3342600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr7:3339800-3340200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:3339800-3340200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:3339800-3340200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:3339800-3340200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
16	chr7:3339800-3340200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:3339800-3340200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:3339800-3340200	Bivalent Enhancer	Primary B cells from cord blood	blood
19	chr7:3339800-3340200	Bivalent Enhancer	Primary T cells from cord blood	blood
20	chr7:3339800-3340200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:3339800-3340200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr7:3339800-3340200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:3339800-3340200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:3339800-3340200	Enhancers	Liver	Liver
25	chr7:3339800-3340200	Enhancers	Brain Angular Gyrus	brain
26	chr7:3339800-3340200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr7:3339800-3340200	Bivalent Enhancer	Fetal Lung	lung
28	chr7:3339800-3340200	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr7:3339800-3340200	Flanking Active TSS	Pancreas	Pancrea
30	chr7:3339800-3340200	Flanking Active TSS	Right Ventricle	heart
31	chr7:3339800-3340200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr7:3339800-3340200	Bivalent Enhancer	Thymus	Thymus
33	chr7:3339800-3340400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr7:3339800-3340400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:3339800-3340400	Enhancers	Primary hematopoietic stem cells	blood
36	chr7:3339800-3340400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr7:3339800-3340400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:3339800-3340400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:3339800-3340400	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr7:3339800-3340600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr7:3339800-3340600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr7:3339800-3340600	Active TSS	Brain Substantia Nigra	brain
43	chr7:3339800-3340600	Enhancers	Fetal Brain Male	brain
44	chr7:3339800-3341600	Active TSS	Fetal Brain Female	brain
45	chr7:3339800-3342200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:3339800-3342200	Active TSS	HSMMtube	muscle
47	chr7:3340000-3340200	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr7:3340000-3340200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:3340000-3340200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr7:3340000-3340200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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