Variant report

Variant	rs1517675
Chromosome Location	chr4:48778936-48778937
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	chr4:48774500..48780275-chr4:48780685..48784374,5	MCF-7	breast:
2	chr4:48772120..48774246-chr4:48777185..48779870,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

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

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

rs_ID	r²[population]
rs10938546	1.00[CHB][hapmap]
rs12502095	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505376	0.92[AMR][1000 genomes]
rs12509766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1712762	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17610398	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17610725	1.00[CHB][hapmap]
rs17656189	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17656727	1.00[CHB][hapmap]
rs17656763	1.00[CHB][hapmap]
rs2304387	1.00[CHB][hapmap]
rs6447646	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6447674	1.00[CHB][hapmap]
rs6825104	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs746513	1.00[CHB][hapmap]
rs776582	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs776586	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs776593	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs776594	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs776596	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs776597	1.00[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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
9	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
3	chr4:48763000-48779800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:48764600-48779800	Weak transcription	HSMM	muscle
5	chr4:48766600-48779800	Weak transcription	Ovary	ovary
6	chr4:48767000-48779800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:48768600-48780000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:48768600-48780800	Weak transcription	Gastric	stomach
10	chr4:48768800-48780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:48768800-48780000	Weak transcription	Colonic Mucosa	Colon
12	chr4:48769400-48779800	Weak transcription	Pancreas	Pancrea
13	chr4:48769600-48780400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:48770000-48779800	Weak transcription	Esophagus	oesophagus
15	chr4:48770200-48779400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:48771600-48779000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:48772800-48780400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:48773000-48779800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:48773200-48779800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:48773400-48780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:48773800-48779200	Weak transcription	Aorta	Aorta
22	chr4:48773800-48779400	Weak transcription	Hela-S3	cervix
23	chr4:48774200-48779200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:48775800-48779000	Weak transcription	NHLF	lung
25	chr4:48776000-48779400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:48776000-48779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:48776000-48779800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:48776000-48779800	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:48776000-48779800	Weak transcription	Spleen	Spleen
30	chr4:48776000-48780800	Weak transcription	Lung	lung
31	chr4:48776200-48780400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:48776600-48779800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:48776600-48780000	Enhancers	Liver	Liver
34	chr4:48776600-48780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:48776800-48780400	Enhancers	Fetal Heart	heart
36	chr4:48777000-48779000	Enhancers	Brain Anterior Caudate	brain
37	chr4:48777000-48779000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr4:48777000-48779000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr4:48777000-48779200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:48777000-48779200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:48777000-48779200	Enhancers	K562	blood
42	chr4:48777000-48779800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr4:48777000-48779800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:48777000-48779800	Enhancers	Colon Smooth Muscle	Colon
45	chr4:48777000-48779800	Enhancers	Fetal Lung	lung
46	chr4:48777000-48780000	Enhancers	HepG2	liver
47	chr4:48777000-48780400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr4:48777200-48779000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr4:48777200-48779000	Enhancers	Brain Germinal Matrix	brain
50	chr4:48777200-48779000	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links