Variant report

Variant	rs9885887
Chromosome Location	chr6:140384438-140384439
allele	C/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	JUN	chr6:140384340-140384473	K562	blood:	n/a	n/a
2	NFIC	chr6:140382792-140384453	SK-N-SH	brain:	n/a	chr6:140383691-140383708
3	POLR2A	chr6:140384326-140384443	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr6:140382705-140384533	SK-N-SH	brain:	n/a	chr6:140383081-140383097 chr6:140383079-140383100 chr6:140384104-140384112 chr6:140383086-140383093 chr6:140383086-140383093 chr6:140383086-140383093
5	MAFK	chr6:140382869-140384442	Hela-S3	cervix:	n/a	chr6:140383916-140383927
6	EP300	chr6:140382710-140384724	SK-N-SH	brain:	n/a	chr6:140383430-140383444

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:139692663..139698708-chr6:140381231..140386402,5	MCF-7	breast:
2	chr6:139695333..139696910-chr6:140382949..140384930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236013	TF binding region
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13362768	1.00[AMR][1000 genomes]
rs6570389	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6902659	1.00[AMR][1000 genomes]
rs6937739	1.00[AMR][1000 genomes]
rs73775460	1.00[EUR][1000 genomes]
rs7746257	1.00[AMR][1000 genomes]
rs7746402	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7747450	1.00[AMR][1000 genomes]
rs7748387	1.00[AMR][1000 genomes]
rs7750737	1.00[AMR][1000 genomes]
rs7762281	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7774903	1.00[AMR][1000 genomes]
rs9484341	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484344	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484345	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484346	1.00[AMR][1000 genomes]
rs9495639	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9495643	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9495665	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3473486	chr6:140380637-140392373	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	esv3473487	chr6:140380684-140392349	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	esv3473488	chr6:140380690-140392319	Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	esv3473489	chr6:140380774-140392251	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140379800-140385200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:140380000-140385200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:140380000-140385800	Enhancers	NHDF-Ad	bronchial
4	chr6:140380600-140386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:140380800-140385000	Enhancers	NHLF	lung
6	chr6:140381000-140384600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:140381000-140385200	Enhancers	HSMM	muscle
8	chr6:140381200-140385800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:140381800-140385000	Enhancers	Osteobl	bone
10	chr6:140382000-140384600	Enhancers	NHEK	skin
11	chr6:140382200-140384600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:140382200-140384600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:140382200-140384600	Enhancers	Fetal Lung	lung
14	chr6:140382400-140384800	Enhancers	Adipose Nuclei	Adipose
15	chr6:140382400-140386400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr6:140382600-140384800	Enhancers	Fetal Heart	heart
17	chr6:140383000-140384600	Enhancers	Fetal Intestine Large	intestine
18	chr6:140383000-140384600	Enhancers	Fetal Kidney	kidney
19	chr6:140383200-140384600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:140383200-140384600	Enhancers	Rectal Smooth Muscle	rectum
21	chr6:140383200-140385600	Weak transcription	Ovary	ovary
22	chr6:140383400-140384600	Enhancers	Fetal Intestine Small	intestine
23	chr6:140383600-140384600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr6:140383800-140384600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:140383800-140384600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:140383800-140384600	Enhancers	NH-A	brain
27	chr6:140384000-140384800	Enhancers	Hela-S3	cervix
28	chr6:140384200-140384600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:140384200-140385800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:140384200-140391400	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:140384400-140384600	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr6:140384400-140384600	Enhancers	HSMMtube	muscle
33	chr6:140384400-140385800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:140384400-140385800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:140384400-140389600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:140384400-140391800	Weak transcription	Fetal Stomach	stomach
37	chr6:140384400-140391800	Weak transcription	Stomach Mucosa	stomach
38	chr6:140384400-140392800	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links