Variant report

Variant	rs4391122
Chromosome Location	chr5:60598543-60598544
allele	A/G
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	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60596613..60601643-chr5:60625817..60629986,6	MCF-7	breast:
3	chr5:60456737..60461436-chr5:60596585..60603587,8	MCF-7	breast:
4	chr5:60593618..60596553-chr5:60596973..60598822,2	K562	blood:
5	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:
6	chr5:60457408..60460091-chr5:60596786..60599332,3	MCF-7	breast:
7	chr5:60595107..60599156-chr5:60625279..60628331,4	K562	blood:
8	chr5:60596572..60599250-chr5:60605731..60609279,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12523278	0.88[YRI][hapmap]
rs4132385	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4352559	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4421060	0.98[ASN][1000 genomes]
rs4546329	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4583848	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4604142	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs4700418	0.85[CEU][hapmap]
rs6449525	1.00[ASN][1000 genomes]
rs6449526	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6449527	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6449528	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs6860599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6867278	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6889338	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6890684	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7701440	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs7724551	0.85[CEU][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60594000-60602400	Enhancers	NHDF-Ad	bronchial
2	chr5:60594000-60602800	Enhancers	HMEC	breast
3	chr5:60594400-60599200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:60595000-60599600	Weak transcription	Fetal Thymus	thymus
5	chr5:60595400-60598800	Weak transcription	Ovary	ovary
6	chr5:60596400-60598600	Enhancers	Brain Germinal Matrix	brain
7	chr5:60596800-60601800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:60597000-60598800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:60597000-60599000	Enhancers	Fetal Heart	heart
10	chr5:60597000-60599000	Enhancers	Fetal Intestine Large	intestine
11	chr5:60597000-60599200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:60597000-60599600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:60597000-60605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:60597200-60598600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:60597200-60598600	Enhancers	Brain Substantia Nigra	brain
16	chr5:60597200-60598600	Flanking Active TSS	HepG2	liver
17	chr5:60597200-60598800	Enhancers	Fetal Intestine Small	intestine
18	chr5:60597200-60598800	Enhancers	Fetal Muscle Leg	muscle
19	chr5:60597200-60598800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr5:60597200-60598800	Enhancers	Stomach Mucosa	stomach
21	chr5:60597200-60599000	Enhancers	Placenta	Placenta
22	chr5:60597200-60599200	Enhancers	Brain Hippocampus Middle	brain
23	chr5:60597200-60599200	Enhancers	Colon Smooth Muscle	Colon
24	chr5:60597200-60599200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr5:60597200-60599800	Enhancers	Adipose Nuclei	Adipose
26	chr5:60597200-60599800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr5:60597400-60598600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:60597400-60598600	Enhancers	Aorta	Aorta
29	chr5:60597400-60598600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:60597400-60598600	Active TSS	Fetal Brain Male	brain
31	chr5:60597400-60598600	Enhancers	Psoas Muscle	Psoas
32	chr5:60597400-60598600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr5:60597400-60598800	Enhancers	Brain Anterior Caudate	brain
34	chr5:60597400-60598800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr5:60597400-60598800	Flanking Active TSS	Fetal Lung	lung
36	chr5:60597400-60599000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:60597400-60599000	Enhancers	Fetal Stomach	stomach
38	chr5:60597600-60599000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:60597600-60599600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:60597600-60599800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr5:60597800-60598800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:60597800-60599000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr5:60597800-60600400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:60598000-60598600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:60598000-60598800	Enhancers	Brain Cingulate Gyrus	brain
46	chr5:60598000-60599000	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr5:60598000-60599000	Flanking Active TSS	HSMM	muscle
48	chr5:60598000-60599200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:60598000-60599800	Flanking Active TSS	A549	lung
50	chr5:60598000-60599800	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links