Variant report

Variant	rs839615
Chromosome Location	chr1:120255578-120255579
allele	C/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	chr1:120229496..120231621-chr1:120254696..120256885,2	K562	blood:
2	chr1:120188760..120191651-chr1:120254416..120257641,3	K562	blood:
3	chr1:120188760..120191459-chr1:120254916..120257641,2	K562	blood:
4	chr1:120253275..120257099-chr1:120276679..120281090,4	K562	blood:
5	chr1:120186762..120190857-chr1:120254727..120257522,5	MCF-7	breast:
6	chr1:120255317..120256884-chr1:120262274..120265030,2	K562	blood:
7	chr1:120254553..120256088-chr2:64878581..64881512,2	K562	blood:
8	chr1:120201333..120204049-chr1:120254351..120256217,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000179833	Chromatin interaction
ENSG00000092621	Chromatin interaction
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10923887	0.84[EUR][1000 genomes]
rs481357	0.90[JPT][hapmap]
rs541763	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550174	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs573763	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs586650	0.95[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs598100	0.95[JPT][hapmap]
rs620741	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636101	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646124	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs663807	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs667770	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839613	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839616	0.89[ASN][1000 genomes]

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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv3417273	chr1:120254479-120256427	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120254200-120255600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:120254200-120255600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:120254200-120255600	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:120254200-120255600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:120254200-120255600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr1:120254200-120255600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:120254200-120255600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:120254200-120255600	Active TSS	Brain Germinal Matrix	brain
9	chr1:120254200-120255600	Active TSS	Fetal Brain Female	brain
10	chr1:120254200-120255600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:120254200-120255600	Active TSS	Fetal Lung	lung
12	chr1:120254200-120255600	Active TSS	Fetal Stomach	stomach
13	chr1:120254200-120255600	Active TSS	Thymus	Thymus
14	chr1:120254200-120255600	Active TSS	HSMM	muscle
15	chr1:120254200-120255600	Active TSS	NH-A	brain
16	chr1:120254200-120255600	Active TSS	Osteobl	bone
17	chr1:120254200-120255800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:120254200-120255800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:120254200-120255800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:120254200-120255800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:120254200-120255800	Active TSS	Aorta	Aorta
22	chr1:120254200-120255800	Active TSS	Brain Hippocampus Middle	brain
23	chr1:120254200-120255800	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:120254200-120255800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:120254200-120255800	Active TSS	Colon Smooth Muscle	Colon
26	chr1:120254200-120255800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr1:120254200-120255800	Active TSS	Fetal Intestine Large	intestine
28	chr1:120254200-120255800	Active TSS	Fetal Kidney	kidney
29	chr1:120254200-120255800	Active TSS	Ovary	ovary
30	chr1:120254200-120255800	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:120254200-120255800	Active TSS	NHLF	lung
32	chr1:120254200-120256000	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr1:120254200-120256000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr1:120254200-120256000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:120254200-120256000	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:120254200-120256000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:120254200-120256000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr1:120254200-120256000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:120254200-120256000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr1:120254200-120256000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:120254200-120256000	Active TSS	Brain Angular Gyrus	brain
42	chr1:120254200-120256000	Active TSS	Brain Anterior Caudate	brain
43	chr1:120254200-120256000	Active TSS	Brain Substantia Nigra	brain
44	chr1:120254200-120256000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
45	chr1:120254200-120256200	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr1:120254200-120256200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr1:120254200-120256200	Active TSS	GM12878-XiMat	blood
48	chr1:120254200-120256600	Active TSS	H9 Cell Line	embryonic stem cell
49	chr1:120254200-120256600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:120254200-120256800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links