Variant report

Variant	rs57959933
Chromosome Location	chr13:51866225-51866226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51865697..51869236-chr13:52025777..52029444,4	K562	blood:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs9535636	0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57959933	INTS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51846400-51866400	Weak transcription	Fetal Brain Male	brain
2	chr13:51851000-51866400	Weak transcription	Adipose Nuclei	Adipose
3	chr13:51853000-51889600	Weak transcription	Brain Angular Gyrus	brain
4	chr13:51854600-51866800	Weak transcription	Stomach Mucosa	stomach
5	chr13:51855600-51875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:51855800-51866400	Weak transcription	Brain Germinal Matrix	brain
7	chr13:51857000-51867000	Weak transcription	Right Ventricle	heart
8	chr13:51857000-51871400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr13:51860800-51867200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:51862400-51870800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:51862800-51867000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:51864800-51867400	Enhancers	Rectal Smooth Muscle	rectum
13	chr13:51865000-51866800	Enhancers	HepG2	liver
14	chr13:51865000-51867600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr13:51865000-51867600	Enhancers	Fetal Heart	heart
16	chr13:51865200-51867200	Enhancers	Colon Smooth Muscle	Colon
17	chr13:51865400-51866800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:51865400-51866800	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr13:51865400-51866800	Enhancers	Brain Substantia Nigra	brain
20	chr13:51865400-51867000	Enhancers	Brain Cingulate Gyrus	brain
21	chr13:51865400-51867400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr13:51865400-51867600	Enhancers	Ovary	ovary
23	chr13:51865400-51867600	Enhancers	Pancreas	Pancrea
24	chr13:51865600-51867000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:51865600-51867000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:51865600-51867000	Enhancers	Brain Hippocampus Middle	brain
27	chr13:51865600-51867000	Enhancers	Osteobl	bone
28	chr13:51865600-51867200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr13:51865600-51867200	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr13:51865600-51867200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr13:51865600-51867200	Enhancers	Brain Anterior Caudate	brain
32	chr13:51865600-51867200	Enhancers	Fetal Lung	lung
33	chr13:51865800-51866400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr13:51865800-51866400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:51865800-51866600	Enhancers	HSMM	muscle
36	chr13:51865800-51866800	Weak transcription	Left Ventricle	heart
37	chr13:51865800-51866800	Enhancers	NH-A	brain
38	chr13:51865800-51867000	Enhancers	HSMMtube	muscle
39	chr13:51865800-51867400	Enhancers	A549	lung
40	chr13:51866000-51866600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
41	chr13:51866000-51866800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr13:51866000-51866800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:51866000-51866800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr13:51866200-51866800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr13:51866200-51867000	Weak transcription	Aorta	Aorta
46	chr13:51866200-51867400	Enhancers	Stomach Smooth Muscle	stomach
47	chr13:51866200-51871200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr13:51866200-51871400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links