Variant report

Variant	rs240390
Chromosome Location	chr6:75973264-75973265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:75952128..75954360-chr6:75971473..75973567,2	K562	blood:
2	chr6:75952128..75954360-chr6:75971385..75973567,3	K562	blood:
3	chr6:75972939..75974519-chr6:75996831..75999415,2	K562	blood:
4	chr6:75965173..75970127-chr6:75970180..75976359,8	K562	blood:

Variant related genes	Relation type
ENSG00000112695	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs117512	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1203213	0.87[EUR][1000 genomes]
rs147523	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs15616	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886411	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs240367	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs240369	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs240374	0.92[JPT][hapmap]
rs240381	0.87[EUR][1000 genomes]
rs240382	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240383	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs240385	0.87[EUR][1000 genomes]
rs240386	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240389	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240392	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240393	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240396	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240398	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs240400	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240401	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs240402	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240403	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240404	0.87[EUR][1000 genomes]
rs240405	0.92[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs240409	0.82[EUR][1000 genomes]
rs240410	0.92[EUR][1000 genomes]
rs240423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240424	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240425	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs240429	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240430	0.87[EUR][1000 genomes]
rs240431	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756794	0.87[ASN][1000 genomes]
rs3777512	0.81[ASN][1000 genomes]
rs381141	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs3822870	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs397039	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs414624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418485	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs429746	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs448854	0.87[EUR][1000 genomes]
rs507912	0.85[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs638590	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs643707	0.82[EUR][1000 genomes]
rs654428	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs683943	0.85[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7741596	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75953800-75978200	Weak transcription	Gastric	stomach
2	chr6:75953800-75982200	Weak transcription	Spleen	Spleen
3	chr6:75954000-75974000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:75954200-75978000	Weak transcription	Pancreas	Pancrea
5	chr6:75954200-75978000	Weak transcription	Small Intestine	intestine
6	chr6:75954200-75978000	Weak transcription	Stomach Mucosa	stomach
7	chr6:75954200-75978200	Weak transcription	Esophagus	oesophagus
8	chr6:75954200-75978400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:75954400-75976800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:75954400-75977200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:75954400-75977600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:75954400-75978000	Weak transcription	Right Ventricle	heart
13	chr6:75954400-75978000	Weak transcription	Hela-S3	cervix
14	chr6:75954400-75986000	Weak transcription	Brain Germinal Matrix	brain
15	chr6:75954600-75982400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:75954800-75982200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:75954800-75988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:75959800-75977400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:75960600-75981400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:75961400-75974000	Strong transcription	HSMM	muscle
21	chr6:75961400-75975400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:75961600-75978200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:75962400-75975200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:75962400-75977600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:75962800-75974000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr6:75962800-75974200	Strong transcription	Adipose Nuclei	Adipose
27	chr6:75962800-75974800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:75962800-75975000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr6:75962800-75975600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr6:75963000-75976800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:75963200-75975600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:75963200-75976000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:75963400-75974600	Strong transcription	Osteobl	bone
34	chr6:75963400-75975800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:75963600-75974200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:75963600-75974400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:75963600-75974400	Strong transcription	Fetal Thymus	thymus
38	chr6:75963600-75975200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:75963800-75975800	Strong transcription	Dnd41	blood
40	chr6:75964000-75976200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:75964600-75974200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr6:75964800-75975600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:75964800-75975800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:75965000-75973800	Strong transcription	GM12878-XiMat	blood
45	chr6:75965000-75974200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:75965000-75974200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr6:75965000-75974600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:75965200-75974000	Strong transcription	Primary B cells from cord blood	blood
49	chr6:75965200-75974000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:75965200-75975400	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links