Variant report

Variant	rs3007410
Chromosome Location	chr1:246742157-246742158
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	chr1:246729017..246731987-chr1:246738180..246742192,5	MCF-7	breast:
2	chr1:226185428..226188059-chr1:246740463..246742577,2	K562	blood:

Variant related genes	Relation type
ENSG00000143751	Chromatin interaction
ENSG00000162852	Chromatin interaction
ENSG00000162851	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10802430	1.00[ASN][1000 genomes]
rs3006079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006080	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3124073	1.00[ASN][1000 genomes]
rs3124074	1.00[ASN][1000 genomes]
rs3129560	1.00[ASN][1000 genomes]
rs34936435	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	nsv527464	chr1:246698653-246742157	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	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
23	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
24	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
25	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
26	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
27	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
28	nsv9047	chr1:246739215-246742538	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3007410	C15orf43	trans	cerebellum	SCAN
rs3007410	ZNF695	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246730800-246744000	Weak transcription	Ovary	ovary
2	chr1:246731000-246747000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:246731400-246746000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:246731400-246746200	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:246731400-246747200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:246731400-246753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:246731600-246747000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:246732000-246746400	Weak transcription	Hela-S3	cervix
9	chr1:246732000-246747600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:246733200-246745600	Weak transcription	Pancreas	Pancrea
11	chr1:246733200-246746000	Weak transcription	Lung	lung
12	chr1:246733200-246747000	Weak transcription	NHEK	skin
13	chr1:246733400-246746800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:246733600-246744000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:246733600-246745400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:246733600-246746800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:246733800-246742200	Weak transcription	Fetal Kidney	kidney
18	chr1:246733800-246742400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:246733800-246742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:246733800-246745800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:246733800-246746200	Weak transcription	Dnd41	blood
22	chr1:246734000-246745600	Weak transcription	Colonic Mucosa	Colon
23	chr1:246734200-246742600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:246735200-246742600	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:246735200-246743000	Weak transcription	HUVEC	blood vessel
26	chr1:246735200-246743200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:246735600-246747200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:246735600-246754800	Weak transcription	Spleen	Spleen
29	chr1:246736600-246745400	Weak transcription	Thymus	Thymus
30	chr1:246736800-246742400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:246737400-246742200	Weak transcription	Adipose Nuclei	Adipose
32	chr1:246738000-246753400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:246738200-246742600	Weak transcription	Placenta	Placenta
34	chr1:246738400-246742800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:246738400-246745000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:246739000-246806200	Weak transcription	Aorta	Aorta
37	chr1:246739600-246745600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:246740000-246742200	Enhancers	Fetal Thymus	thymus
39	chr1:246740000-246743400	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:246740000-246744600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:246740200-246742400	Enhancers	HepG2	liver
42	chr1:246740200-246742800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:246740400-246747600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr1:246740600-246742200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:246740600-246743400	Enhancers	Osteobl	bone
46	chr1:246740600-246744600	Enhancers	Rectal Smooth Muscle	rectum
47	chr1:246740600-246744600	Enhancers	NHDF-Ad	bronchial
48	chr1:246740600-246748400	Enhancers	Colon Smooth Muscle	Colon
49	chr1:246740800-246742600	Weak transcription	Small Intestine	intestine
50	chr1:246740800-246743000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links