Variant report

Variant	rs35988237
Chromosome Location	chr5:179478528-179478529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179232497..179234437-chr5:179477611..179480495,2	K562	blood:
2	chr5:179478110..179479626-chr5:179490709..179493377,2	K562	blood:
3	chr5:179429959..179431580-chr5:179476627..179479409,2	K562	blood:
4	chr5:179477610..179479379-chr5:179497393..179499345,2	K562	blood:
5	chr5:179477454..179480172-chr5:179480653..179484113,3	MCF-7	breast:
6	chr5:179279889..179282788-chr5:179478192..179480009,2	K562	blood:
7	chr5:179473631..179475664-chr5:179477740..179480217,2	K562	blood:
8	chr5:179474733..179479669-chr5:179495487..179500173,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1102191	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12519642	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12654148	0.88[AMR][1000 genomes]
rs12656814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13161895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13166286	0.91[AFR][1000 genomes]
rs13179406	0.91[AFR][1000 genomes]
rs17079966	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17079968	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248318	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs248320	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs27012	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs27018	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34027780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34603792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34674199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35135297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35592104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35608303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35973843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3719	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs379655	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3797763	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3797764	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs394616	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4129403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4235504	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs438050	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4389651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs442181	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4700853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs594202	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6873781	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6873994	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6876648	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71613436	0.91[AFR][1000 genomes]
rs71613437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71613438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857187	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs857188	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs864482	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
7	chr5:179467400-179483200	Weak transcription	HSMM	muscle
8	chr5:179467800-179479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
10	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
11	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
12	chr5:179473600-179479000	Weak transcription	Spleen	Spleen
13	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
15	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
16	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
17	chr5:179474800-179478800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:179475200-179481600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr5:179475400-179479400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:179475600-179479200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:179475800-179483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:179476000-179478800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr5:179476000-179481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:179476000-179484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:179476000-179497800	Weak transcription	Lung	lung
26	chr5:179476200-179479200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:179476400-179481400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:179476400-179486200	Weak transcription	Ovary	ovary
29	chr5:179476400-179487000	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
31	chr5:179476800-179480200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:179477200-179479000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:179477200-179479200	Weak transcription	Fetal Heart	heart
34	chr5:179477200-179480000	Weak transcription	Fetal Lung	lung
35	chr5:179477400-179478800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr5:179477400-179479000	Weak transcription	Fetal Brain Female	brain
37	chr5:179477400-179480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:179477400-179480200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:179477400-179481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:179477400-179483800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:179477400-179495000	Weak transcription	Gastric	stomach
43	chr5:179477600-179478600	Weak transcription	Brain Angular Gyrus	brain
44	chr5:179477600-179478800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:179477600-179479000	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:179477600-179479200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:179477600-179479200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:179477600-179479200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:179477600-179479200	Weak transcription	K562	blood
50	chr5:179477600-179479800	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links