Variant report

Variant	rs9390172
Chromosome Location	chr6:144903517-144903518
allele	A/C
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	CTCF	chr6:144902718-144903738	SK-N-SH	brain:	n/a	chr6:144903160-144903168
2	CCNT2	chr6:144903392-144903521	K562	blood:	n/a	n/a
3	RAD21	chr6:144902480-144903787	SK-N-SH	brain:	n/a	chr6:144903123-144903142
4	GATA3	chr6:144903400-144903677	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr6:144902391-144904894	SK-N-SH	brain:	n/a	chr6:144903652-144903660 chr6:144904875-144904889 chr6:144902630-144902640
6	MEF2A	chr6:144903198-144903646	K562	blood:	n/a	chr6:144903511-144903526 chr6:144903466-144903480
7	MXI1	chr6:144902889-144905090	SK-N-SH	brain:	n/a	n/a
8	SMC3	chr6:144902741-144903650	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:144902620..144903603-chr6:145535345..145536293,3	K562	blood:
2	chr6:144902631..144903701-chr6:145252294..145253338,4	K562	blood:
3	chr6:144902617..144903608-chr6:146025327..146026043,2	MCF-7	breast:

Variant related genes	Relation type
UTRN	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12661566	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12663647	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12664494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12664819	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534442	0.87[JPT][hapmap]
rs1534443	0.87[JPT][hapmap]
rs1534444	0.87[JPT][hapmap]
rs17073972	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1918751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997252	0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091486	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811100	0.96[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4076068	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896728	1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[ASN][1000 genomes]
rs6906465	0.87[JPT][hapmap]
rs9321980	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9373415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9376823	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376824	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9376826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9376828	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9386070	0.88[ASN][1000 genomes]
rs9386071	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9386072	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9386073	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9390170	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9390174	0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9390175	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9390176	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9390178	0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9390184	0.83[JPT][hapmap]
rs9399480	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9399481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403563	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9403564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403567	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9403572	0.83[JPT][hapmap]
rs9497009	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:144857200-144904000	Weak transcription	Psoas Muscle	Psoas
4	chr6:144867400-144903800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:144873000-144903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:144874000-144904200	Weak transcription	Placenta	Placenta
7	chr6:144877000-144904200	Weak transcription	Fetal Stomach	stomach
8	chr6:144879200-144904000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:144881800-144937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:144885400-144903800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:144885800-144943400	Weak transcription	Ovary	ovary
12	chr6:144888800-144904000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:144895200-144904000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:144896600-144903800	Weak transcription	Brain Anterior Caudate	brain
15	chr6:144897400-144904000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:144898200-144903800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:144898400-144904200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:144898600-144903800	Weak transcription	GM12878-XiMat	blood
19	chr6:144898600-144904000	Weak transcription	Right Ventricle	heart
20	chr6:144898600-144904400	Weak transcription	Fetal Intestine Large	intestine
21	chr6:144898600-144912800	Weak transcription	Gastric	stomach
22	chr6:144899600-144904000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:144899600-144904200	Weak transcription	Small Intestine	intestine
24	chr6:144899600-144904200	Weak transcription	Spleen	Spleen
25	chr6:144899600-144909000	Weak transcription	Aorta	Aorta
26	chr6:144899600-144913800	Weak transcription	Lung	lung
27	chr6:144899600-144931800	Weak transcription	Esophagus	oesophagus
28	chr6:144899800-144914400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:144899800-144914400	Weak transcription	Fetal Intestine Small	intestine
30	chr6:144899800-144917400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:144900000-144903800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:144900000-144903800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:144900000-144903800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:144900000-144904000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:144900000-144904000	Weak transcription	Left Ventricle	heart
36	chr6:144900000-144904000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:144900000-144904200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:144900000-144915400	Weak transcription	Pancreas	Pancrea
39	chr6:144900600-144903600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:144901800-144903800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:144901800-144904200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:144902000-144903800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:144902200-144903800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr6:144902200-144904200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:144902400-144908400	Weak transcription	HUVEC	blood vessel
46	chr6:144902600-144904000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:144902800-144903800	Enhancers	Fetal Heart	heart
48	chr6:144902800-144904000	Enhancers	Adipose Nuclei	Adipose
49	chr6:144902800-144904000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:144903000-144903800	Enhancers	Primary T cells from cord blood	blood

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