Variant report

Variant	rs56260303
Chromosome Location	chr3:93820698-93820699
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	STAT3	chr3:93820697-93820897	MCF10A-Er-Src	breast:	n/a	n/a
2	FOSL2	chr3:93820616-93821130	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr3:93820680-93820830	HRE	kidney:	n/a	n/a
4	E2F4	chr3:93820649-93820849	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr3:93820660-93820910	HPF	lung:	n/a	chr3:93820866-93820884 chr3:93820861-93820882
6	RFX5	chr3:93820482-93821253	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr3:93820639-93821130	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:93818192..93820955-chr3:93826379..93828481,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-108P	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10433405	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934674	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934676	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364604	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61739170	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62265480	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62265486	0.89[EUR][1000 genomes]
rs62265488	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62266146	0.84[EUR][1000 genomes]
rs62266147	0.81[EUR][1000 genomes]
rs62266150	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62266151	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62266152	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7432837	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8178591	0.84[EUR][1000 genomes]
rs8178607	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93782800-93848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:93782800-93849400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:93783200-93824600	Weak transcription	NHEK	skin
4	chr3:93783200-93851600	Weak transcription	HMEC	breast
5	chr3:93783400-93833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:93783600-93837800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:93785600-93834400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:93786200-93834600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:93786400-93830800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:93786800-93849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:93791400-93841200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:93792200-93833200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:93795600-93822000	Weak transcription	HSMMtube	muscle
14	chr3:93795600-93847000	Weak transcription	Osteobl	bone
15	chr3:93796000-93857800	Weak transcription	Fetal Brain Male	brain
16	chr3:93799000-93851600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:93800000-93830800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:93800200-93851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:93802200-93830800	Weak transcription	Fetal Kidney	kidney
20	chr3:93802400-93849600	Weak transcription	Stomach Mucosa	stomach
21	chr3:93802600-93851800	Weak transcription	Small Intestine	intestine
22	chr3:93802800-93830800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:93803000-93826600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:93803400-93835800	Weak transcription	Psoas Muscle	Psoas
25	chr3:93804400-93834600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:93804800-93833000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:93805000-93825800	Weak transcription	Fetal Intestine Small	intestine
28	chr3:93806400-93820800	Weak transcription	HSMM	muscle
29	chr3:93806400-93834800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:93808400-93849600	Weak transcription	Fetal Heart	heart
31	chr3:93808600-93830800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:93811400-93832800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:93812200-93821600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:93812200-93826800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:93812400-93852200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:93813000-93823400	Strong transcription	Dnd41	blood
37	chr3:93813000-93824600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:93814200-93831400	Weak transcription	A549	lung
39	chr3:93814400-93824600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:93814600-93845200	Weak transcription	Esophagus	oesophagus
41	chr3:93814600-93847000	Weak transcription	Spleen	Spleen
42	chr3:93814600-93849400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:93814600-93849400	Weak transcription	Right Ventricle	heart
44	chr3:93814600-93849600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:93814600-93849800	Weak transcription	Colonic Mucosa	Colon
46	chr3:93814800-93845200	Weak transcription	Gastric	stomach
47	chr3:93814800-93857800	Weak transcription	Pancreas	Pancrea
48	chr3:93815400-93834200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:93815600-93822000	Weak transcription	Fetal Brain Female	brain
50	chr3:93815600-93825800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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