Variant report

Variant	rs4896580
Chromosome Location	chr6:142476836-142476837
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142475480..142479893-chr6:142481592..142484800,4	K562	blood:
2	chr6:142475754..142477971-chr6:142621259..142624312,3	MCF-7	breast:
3	chr6:142476386..142478985-chr6:142483280..142485789,2	MCF-7	breast:
4	chr6:142475480..142477535-chr6:142483300..142485466,2	K562	blood:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1931996	0.84[CEU][hapmap]
rs1989181	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs225648	0.84[JPT][hapmap]
rs225699	0.84[JPT][hapmap]
rs3811083	0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs6570497	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6902780	0.80[CHB][hapmap];0.96[YRI][hapmap]
rs6906577	0.82[YRI][hapmap]
rs6940882	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs9373333	0.90[CEU][hapmap]
rs9376675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9385985	1.00[CEU][hapmap]
rs9399394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399395	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9484600	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142468800-142488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:142469200-142477000	Weak transcription	Stomach Mucosa	stomach
3	chr6:142469200-142483400	Weak transcription	Aorta	Aorta
4	chr6:142469200-142487800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:142469600-142487800	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:142469600-142487800	Weak transcription	Thymus	Thymus
7	chr6:142469800-142481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:142469800-142487600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:142470000-142477000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:142470000-142477200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:142470000-142481400	Weak transcription	Gastric	stomach
12	chr6:142470000-142484000	Weak transcription	Psoas Muscle	Psoas
13	chr6:142470000-142486400	Weak transcription	Fetal Intestine Small	intestine
14	chr6:142470200-142484000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:142470200-142487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:142470200-142488200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:142470200-142488200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
19	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
20	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
21	chr6:142470400-142477000	Weak transcription	Adipose Nuclei	Adipose
22	chr6:142470400-142477000	Weak transcription	Brain Substantia Nigra	brain
23	chr6:142470400-142477000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:142470400-142477000	Weak transcription	HSMM	muscle
25	chr6:142470400-142487400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:142470400-142487600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:142470400-142487600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:142470400-142487600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:142470600-142477000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:142470600-142477000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:142470600-142477200	Weak transcription	Small Intestine	intestine
32	chr6:142470600-142483800	Weak transcription	Fetal Lung	lung
33	chr6:142470600-142486000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:142470600-142487600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:142470800-142477000	Weak transcription	Brain Angular Gyrus	brain
36	chr6:142470800-142481400	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:142470800-142487600	Weak transcription	Fetal Intestine Large	intestine
38	chr6:142470800-142487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:142471000-142477200	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:142471600-142485600	Weak transcription	Brain Germinal Matrix	brain
41	chr6:142471800-142477200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:142472000-142487600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:142472400-142477000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:142472400-142477000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:142472400-142477200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:142472400-142477400	Weak transcription	HepG2	liver
47	chr6:142472400-142487800	Weak transcription	Left Ventricle	heart
48	chr6:142472400-142487800	Weak transcription	Ovary	ovary
49	chr6:142472400-142488200	Weak transcription	Primary B cells from cord blood	blood
50	chr6:142472800-142481400	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links