Variant report

Variant	rs9403408
Chromosome Location	chr6:143166001-143166002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143164077..143167005-chr6:143171548..143173289,2	K562	blood:
2	chr6:143164226..143166914-chr6:143265951..143267932,2	MCF-7	breast:
3	chr20:45985147..45987489-chr6:143164648..143166679,2	MCF-7	breast:
4	chr6:143160497..143162652-chr6:143164958..143167111,2	MCF-7	breast:
5	chr6:143148679..143151858-chr6:143163434..143166597,3	K562	blood:
6	chr6:143163087..143164767-chr6:143165602..143167738,2	K562	blood:
7	chr6:143149262..143152050-chr6:143165097..143166681,2	K562	blood:

Variant related genes	Relation type
ENSG00000101040	Chromatin interaction
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1005294	0.84[AMR][1000 genomes]
rs107118	0.81[ASN][1000 genomes]
rs107119	0.81[ASN][1000 genomes]
rs13195550	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13209704	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13211716	0.82[ASN][1000 genomes]
rs2050311	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs28743065	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4896599	0.86[ASN][1000 genomes]
rs5022324	0.87[ASN][1000 genomes]
rs67253362	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6925325	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs728035	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8180684	0.83[ASN][1000 genomes]
rs9376710	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9390025	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9390026	0.83[ASN][1000 genomes]
rs9496470	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9496471	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143144800-143166800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:143162400-143166400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr6:143162400-143166400	Enhancers	Brain Anterior Caudate	brain
4	chr6:143162400-143166800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:143162600-143166800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:143162600-143166800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:143162800-143166600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:143163000-143166800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:143163000-143167400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr6:143163000-143167800	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr6:143163400-143166200	Enhancers	HepG2	liver
12	chr6:143163600-143166800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:143163800-143166400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:143164000-143166200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:143164000-143166400	Enhancers	Brain Hippocampus Middle	brain
16	chr6:143164200-143166200	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:143164200-143166600	Enhancers	HMEC	breast
18	chr6:143164200-143166800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:143164200-143167200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:143164200-143167600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:143164200-143168400	Enhancers	Fetal Thymus	thymus
22	chr6:143164400-143166400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:143164400-143166400	Enhancers	NH-A	brain
24	chr6:143164400-143166600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:143164400-143166800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:143164400-143167000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:143164600-143166200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:143164600-143166600	Enhancers	Fetal Brain Female	brain
29	chr6:143164600-143166800	Enhancers	Thymus	Thymus
30	chr6:143164800-143166200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:143165000-143166400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:143165000-143166800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:143165000-143168400	Enhancers	Dnd41	blood
34	chr6:143165200-143166200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:143165200-143166200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr6:143165200-143166800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:143165200-143166800	Enhancers	Fetal Stomach	stomach
38	chr6:143165200-143167200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:143165200-143167400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:143165200-143168200	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:143165200-143168400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:143165200-143169000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:143165400-143166200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:143165400-143166400	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:143165400-143166400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr6:143165400-143166400	Enhancers	HUVEC	blood vessel
47	chr6:143165400-143166600	Enhancers	Adipose Nuclei	Adipose
48	chr6:143165400-143166600	Enhancers	Brain Substantia Nigra	brain
49	chr6:143165400-143166600	Enhancers	Psoas Muscle	Psoas
50	chr6:143165400-143166600	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links