Variant report

Variant	rs2572347
Chromosome Location	chr4:48896772-48896773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48896623..48898148-chr4:48938034..48940839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251334	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10938545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11729557	0.80[AFR][1000 genomes]
rs2354942	0.87[AFR][1000 genomes]
rs2465262	0.90[AFR][1000 genomes]
rs2572331	1.00[AMR][1000 genomes]
rs2572339	1.00[AMR][1000 genomes]
rs2572340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2572341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2572342	0.90[AFR][1000 genomes]
rs2605253	1.00[AMR][1000 genomes]
rs2712155	0.90[AFR][1000 genomes]
rs2925213	0.98[AFR][1000 genomes]
rs4694905	0.80[AFR][1000 genomes]
rs4695406	0.80[AFR][1000 genomes]
rs6815932	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6824209	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6839713	0.90[AFR][1000 genomes]
rs6844579	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7654729	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7669831	0.80[AFR][1000 genomes]
rs7698768	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48860400-48901400	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:48877800-48897000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:48879400-48907800	Weak transcription	Right Ventricle	heart
4	chr4:48887200-48904200	Weak transcription	Esophagus	oesophagus
5	chr4:48887800-48903800	Weak transcription	Placenta	Placenta
6	chr4:48890600-48906200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:48890800-48896800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:48890800-48898800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:48891000-48898800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:48891000-48904200	Weak transcription	Spleen	Spleen
11	chr4:48891200-48898800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:48891200-48902000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:48891200-48902800	Weak transcription	Fetal Kidney	kidney
14	chr4:48891200-48907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:48891200-48907800	Weak transcription	Fetal Lung	lung
16	chr4:48891400-48902000	Weak transcription	Colonic Mucosa	Colon
17	chr4:48891400-48907800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:48891600-48903000	Weak transcription	Hela-S3	cervix
19	chr4:48891800-48898400	Weak transcription	Small Intestine	intestine
20	chr4:48891800-48899600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:48891800-48901000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:48891800-48901800	Strong transcription	Fetal Thymus	thymus
23	chr4:48891800-48904600	Strong transcription	Liver	Liver
24	chr4:48892000-48899400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:48892000-48899400	Strong transcription	Brain Germinal Matrix	brain
26	chr4:48892000-48900200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:48892000-48900800	Strong transcription	Primary T cells from cord blood	blood
28	chr4:48892000-48901200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:48892000-48901400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:48892000-48901400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:48892000-48901400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:48892000-48902000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr4:48892000-48905400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:48892200-48900200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:48892200-48900600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:48892200-48906600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:48892200-48907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr4:48892400-48897000	Weak transcription	Fetal Brain Male	brain
39	chr4:48892400-48898600	Weak transcription	Brain Anterior Caudate	brain
40	chr4:48892400-48899600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:48892400-48900800	Strong transcription	Primary B cells from cord blood	blood
42	chr4:48892400-48901400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr4:48892400-48903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:48892400-48906800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:48892600-48899400	Strong transcription	Thymus	Thymus
46	chr4:48892600-48901000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:48892600-48901600	Strong transcription	Dnd41	blood
48	chr4:48892600-48906800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr4:48892800-48899400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:48892800-48907000	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links