Variant report

Variant	rs4494115
Chromosome Location	chr1:246747586-246747587
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	chr1:246730131..246732589-chr1:246747162..246749763,2	MCF-7	breast:
2	chr1:246746217..246748591-chr1:246759216..246761418,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12729729	0.96[ASN][1000 genomes]
rs12741150	0.82[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs12756527	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758590	0.82[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs4129249	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs4271182	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61852389	0.86[ASN][1000 genomes]
rs6680646	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7514190	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs7518651	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
18	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
19	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
20	nsv522963	chr1:246696596-246747586	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv873420	chr1:246706139-246755124	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv1014280	chr1:246709243-246823255	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
24	nsv1013264	chr1:246723012-246807400	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv535415	chr1:246723012-246807400	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
26	nsv1005214	chr1:246730885-246841107	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4494115	CPNE7	trans	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246731400-246753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:246732000-246747600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:246735600-246754800	Weak transcription	Spleen	Spleen
4	chr1:246738000-246753400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:246739000-246806200	Weak transcription	Aorta	Aorta
6	chr1:246740400-246747600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:246740600-246748400	Enhancers	Colon Smooth Muscle	Colon
8	chr1:246741200-246750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:246741200-246751000	Weak transcription	HSMMtube	muscle
10	chr1:246742200-246765600	Weak transcription	HSMM	muscle
11	chr1:246742600-246750600	Weak transcription	NH-A	brain
12	chr1:246743000-246753400	Weak transcription	Placenta	Placenta
13	chr1:246743600-246748800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:246744000-246749400	Enhancers	Ovary	ovary
15	chr1:246744000-246754800	Weak transcription	Fetal Brain Female	brain
16	chr1:246744400-246758600	Weak transcription	Fetal Brain Male	brain
17	chr1:246744400-246770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:246744600-246749000	Enhancers	Small Intestine	intestine
19	chr1:246744800-246748800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:246744800-246753400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:246745400-246747800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:246745400-246748800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:246745400-246748800	Strong transcription	Thymus	Thymus
24	chr1:246745600-246748200	Strong transcription	Primary B cells from cord blood	blood
25	chr1:246745600-246748400	Enhancers	Stomach Smooth Muscle	stomach
26	chr1:246745600-246748400	Strong transcription	GM12878-XiMat	blood
27	chr1:246745600-246748600	Enhancers	Left Ventricle	heart
28	chr1:246745600-246748800	Strong transcription	Fetal Thymus	thymus
29	chr1:246745800-246748600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:246745800-246749600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:246745800-246755200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:246746000-246748800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:246746000-246748800	Genic enhancers	Fetal Stomach	stomach
34	chr1:246746000-246749200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:246746200-246747600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:246746200-246748000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:246746200-246748000	Enhancers	Fetal Intestine Large	intestine
38	chr1:246746200-246748200	Strong transcription	Dnd41	blood
39	chr1:246746200-246748600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:246746200-246748600	Enhancers	Brain Hippocampus Middle	brain
41	chr1:246746200-246748800	Enhancers	Brain Substantia Nigra	brain
42	chr1:246746200-246749000	Enhancers	Fetal Muscle Leg	muscle
43	chr1:246746200-246749200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:246746400-246747600	Enhancers	Fetal Kidney	kidney
45	chr1:246746400-246747600	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr1:246746400-246747600	Genic enhancers	NHLF	lung
47	chr1:246746400-246748000	Enhancers	Hela-S3	cervix
48	chr1:246746400-246748200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:246746400-246748400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:246746400-246748800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links