Variant report

Variant	rs9380861
Chromosome Location	chr6:39399535-39399536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:39397690-39399558	SK-N-SH	brain:	n/a	n/a
2	EP300	chr6:39398081-39400728	SK-N-SH	brain:	n/a	chr6:39400634-39400648
3	GATA2	chr6:39398621-39399587	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
KIF6	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10947813	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11961693	0.81[ASN][1000 genomes]
rs11962587	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964924	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11968704	0.81[ASN][1000 genomes]
rs11969059	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11969395	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1410488	0.91[ASN][1000 genomes]
rs1927774	0.91[ASN][1000 genomes]
rs1927775	0.91[ASN][1000 genomes]
rs1952362	0.91[ASN][1000 genomes]
rs2235817	0.81[ASN][1000 genomes]
rs2395727	0.91[ASN][1000 genomes]
rs28533484	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35553201	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4464790	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4482968	0.81[ASN][1000 genomes]
rs4482969	0.81[ASN][1000 genomes]
rs4711598	0.95[ASN][1000 genomes]
rs4714253	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714254	0.91[ASN][1000 genomes]
rs4714255	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59724542	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72850669	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9296299	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9349120	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357305	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357308	0.81[ASN][1000 genomes]
rs9367009	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9367012	0.81[ASN][1000 genomes]
rs9367016	0.81[ASN][1000 genomes]
rs9369117	0.90[ASN][1000 genomes]
rs9380862	0.91[ASN][1000 genomes]
rs9380863	0.92[ASN][1000 genomes]
rs9380864	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380865	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380871	0.81[ASN][1000 genomes]
rs9380872	0.81[ASN][1000 genomes]
rs9380873	0.81[ASN][1000 genomes]
rs9394592	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9394595	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9394600	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9471103	0.91[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	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39395400-39400000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:39397000-39400800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:39397000-39401400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:39397000-39401800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:39397200-39400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:39397400-39401600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:39397600-39400600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:39397600-39400800	Enhancers	Fetal Muscle Leg	muscle
9	chr6:39397800-39399600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:39397800-39400400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:39397800-39400600	Enhancers	Fetal Stomach	stomach
12	chr6:39398000-39399600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr6:39398000-39400600	Enhancers	HSMMtube	muscle
14	chr6:39398200-39399600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:39398200-39399800	Enhancers	Duodenum Mucosa	Duodenum
16	chr6:39398200-39401600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:39398200-39401600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:39398400-39399600	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr6:39398400-39399800	Enhancers	Colon Smooth Muscle	Colon
20	chr6:39398400-39400000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:39398600-39399800	Enhancers	Fetal Muscle Trunk	muscle
22	chr6:39398800-39399600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:39398800-39399600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:39398800-39399600	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr6:39398800-39399600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr6:39398800-39399600	Enhancers	Fetal Brain Female	brain
27	chr6:39398800-39399600	Enhancers	Lung	lung
28	chr6:39398800-39399800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr6:39398800-39399800	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:39398800-39399800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:39398800-39399800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:39398800-39399800	Enhancers	Placenta	Placenta
33	chr6:39398800-39400000	Enhancers	Fetal Thymus	thymus
34	chr6:39398800-39400000	Enhancers	Dnd41	blood
35	chr6:39398800-39400400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:39398800-39400400	Enhancers	HSMM	muscle
37	chr6:39398800-39400800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:39399000-39399600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:39399000-39399600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:39399000-39399600	Enhancers	Primary hematopoietic stem cells	blood
41	chr6:39399000-39399600	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr6:39399000-39399600	Enhancers	Left Ventricle	heart
43	chr6:39399000-39399600	Enhancers	Rectal Smooth Muscle	rectum
44	chr6:39399000-39399600	Enhancers	Stomach Mucosa	stomach
45	chr6:39399000-39399600	Enhancers	Thymus	Thymus
46	chr6:39399000-39400000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:39399000-39400000	Enhancers	NH-A	brain
48	chr6:39399200-39399600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:39399200-39399800	Enhancers	NHEK	skin
50	chr6:39399200-39400400	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links