Variant report

Variant	rs2513899
Chromosome Location	chr8:103798301-103798302
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:103798127..103800585-chr8:103873832..103876657,2	MCF-7	breast:
2	chr8:103643269..103645480-chr8:103797522..103801312,3	MCF-7	breast:
3	chr8:103777223..103779993-chr8:103798108..103799875,2	MCF-7	breast:
4	chr8:103664425..103672321-chr8:103786823..103809844,55	MCF-7	breast:
5	chr8:103668372..103669150-chr8:103798115..103798979,2	MCF-7	breast:
6	chr8:103797710..103802758-chr8:103818497..103821142,6	K562	blood:
7	chr8:103797903..103806624-chr8:103818327..103823736,14	K562	blood:
8	chr8:103656072..103671156-chr8:103783158..103810200,133	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000253669	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000253320	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2436868	0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2436875	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2513897	0.85[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs2513901	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	esv1814245	chr8:103735804-103824566	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv519814	chr8:103778809-103806914	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2513899	GRHL2	cis	cerebellum	SCAN
rs2513899	OSR2	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103786800-103801000	Weak transcription	Small Intestine	intestine
2	chr8:103787200-103799800	Weak transcription	HMEC	breast
3	chr8:103789200-103800400	Weak transcription	Gastric	stomach
4	chr8:103789400-103800000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:103789400-103800400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:103793600-103800800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:103794000-103799000	Weak transcription	Colon Smooth Muscle	Colon
8	chr8:103794200-103801200	Weak transcription	Fetal Kidney	kidney
9	chr8:103794600-103800000	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:103794800-103799800	Weak transcription	Fetal Heart	heart
11	chr8:103795000-103799000	Weak transcription	Lung	lung
12	chr8:103795000-103799800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr8:103795200-103799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:103795200-103799800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:103795200-103799800	Weak transcription	Stomach Mucosa	stomach
16	chr8:103795200-103800000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr8:103795200-103800200	Weak transcription	Aorta	Aorta
18	chr8:103795200-103800200	Weak transcription	Ovary	ovary
19	chr8:103795200-103800200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:103795200-103800400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr8:103795200-103804400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr8:103795600-103799000	Weak transcription	Left Ventricle	heart
23	chr8:103795600-103799000	Weak transcription	HSMMtube	muscle
24	chr8:103795600-103799000	Weak transcription	K562	blood
25	chr8:103795600-103799200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr8:103795600-103799200	Weak transcription	Right Ventricle	heart
27	chr8:103795600-103799800	Weak transcription	Fetal Intestine Large	intestine
28	chr8:103795600-103799800	Weak transcription	Fetal Lung	lung
29	chr8:103795600-103800400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr8:103795600-103801000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr8:103795600-103801000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr8:103795600-103801000	Weak transcription	Primary T cells from cord blood	blood
33	chr8:103795600-103801200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr8:103795600-103803000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr8:103795800-103799000	Weak transcription	Right Atrium	heart
36	chr8:103795800-103799000	Weak transcription	HSMM	muscle
37	chr8:103795800-103799400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr8:103795800-103799800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:103795800-103799800	Weak transcription	Adipose Nuclei	Adipose
40	chr8:103795800-103799800	Weak transcription	Hela-S3	cervix
41	chr8:103795800-103799800	Weak transcription	NHLF	lung
42	chr8:103795800-103800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:103795800-103800000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr8:103795800-103800000	Weak transcription	NHDF-Ad	bronchial
45	chr8:103795800-103800200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr8:103795800-103800200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr8:103795800-103800200	Weak transcription	Pancreas	Pancrea
48	chr8:103795800-103800400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr8:103795800-103800800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr8:103795800-103800800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links