Variant report

Variant	rs6674492
Chromosome Location	chr1:223906113-223906114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
2	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs7412088	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6674492	CAPN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
2	chr1:223901600-223906200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:223901600-223906400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:223901800-223906200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:223902400-223906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:223902400-223906600	Enhancers	Fetal Thymus	thymus
8	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:223903000-223907800	Weak transcription	Liver	Liver
10	chr1:223903200-223906400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:223903200-223907200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:223903400-223906200	Strong transcription	Fetal Kidney	kidney
14	chr1:223903400-223907400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr1:223903400-223908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:223903400-223908800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:223903600-223909400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:223904000-223909000	Genic enhancers	Hela-S3	cervix
21	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
22	chr1:223904200-223906800	Strong transcription	Fetal Lung	lung
23	chr1:223904200-223909800	Genic enhancers	NH-A	brain
24	chr1:223904400-223907400	Genic enhancers	HMEC	breast
25	chr1:223904400-223910000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:223904400-223922400	Genic enhancers	NHLF	lung
28	chr1:223904600-223907200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:223904600-223907600	Weak transcription	Small Intestine	intestine
30	chr1:223904600-223908000	Weak transcription	Thymus	Thymus
31	chr1:223904600-223908600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:223904600-223908600	Weak transcription	Right Atrium	heart
33	chr1:223904600-223909800	Genic enhancers	HUVEC	blood vessel
34	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
35	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
36	chr1:223904800-223906200	Strong transcription	Fetal Intestine Large	intestine
37	chr1:223904800-223906400	Enhancers	Primary T cells from cord blood	blood
38	chr1:223904800-223907400	Strong transcription	K562	blood
39	chr1:223904800-223908000	Genic enhancers	Placenta	Placenta
40	chr1:223904800-223908400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:223904800-223909000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:223904800-223909000	Strong transcription	Brain Angular Gyrus	brain
43	chr1:223904800-223909200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr1:223904800-223909400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:223904800-223909400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:223904800-223909600	Genic enhancers	HSMM	muscle
47	chr1:223904800-223910600	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr1:223904800-223911800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:223904800-223913200	Strong transcription	Fetal Stomach	stomach
50	chr1:223904800-223914000	Genic enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links