Variant report

Variant	rs6688376
Chromosome Location	chr1:154326366-154326367
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154318653..154322078-chr1:154325246..154327386,3	K562	blood:
2	chr1:154326234..154328532-chr1:154330997..154333513,2	MCF-7	breast:
3	chr1:154325023..154326724-chr1:154450877..154451767,6	MCF-7	breast:
4	chr1:154321971..154324545-chr1:154326207..154328422,3	MCF-7	breast:
5	chr1:154296678..154299096-chr1:154324754..154327396,2	K562	blood:
6	chr1:154325628..154327486-chr1:154529705..154532667,2	K562	blood:
7	chr1:154326053..154326761-chr1:154377856..154378554,2	MCF-7	breast:
8	chr1:154190008..154193329-chr1:154323255..154327327,4	K562	blood:
9	chr1:154158325..154158864-chr1:154325830..154326669,2	MCF-7	breast:
10	chr1:154296558..154298616-chr1:154325091..154326672,3	MCF-7	breast:
11	chr1:154317447..154318373-chr1:154325751..154326693,2	K562	blood:
12	chr1:154320515..154323145-chr1:154323844..154326958,4	K562	blood:
13	chr1:154325453..154327893-chr1:154424368..154426017,2	MCF-7	breast:
14	chr1:154298802..154301853-chr1:154325196..154327308,4	MCF-7	breast:
15	chr1:154324756..154327782-chr1:154376990..154379231,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160714	Chromatin interaction
ENSG00000228013	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12077870	0.83[CHB][hapmap]
rs12729561	0.81[JPT][hapmap]
rs6672010	0.93[GIH][hapmap]
rs6702754	0.81[ASW][hapmap];0.93[GIH][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6688376	EFNA3	cis	parietal	SCAN
rs6688376	AEN	trans	parietal	SCAN
rs6688376	CREB3L4	cis	parietal	SCAN
rs6688376	SLC27A3	cis	parietal	SCAN
rs6688376	DENND4B	cis	cerebellum	SCAN
rs6688376	NPR1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154324800-154326400	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr1:154325200-154326400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154325400-154326400	Enhancers	Fetal Heart	heart
4	chr1:154325400-154328200	Enhancers	Hela-S3	cervix
5	chr1:154325600-154326400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:154325600-154326400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr1:154325600-154327000	Weak transcription	Gastric	stomach
8	chr1:154325600-154327200	Enhancers	Lung	lung
9	chr1:154325800-154326400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:154325800-154326400	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:154325800-154326400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:154325800-154326400	Enhancers	Brain Angular Gyrus	brain
13	chr1:154325800-154326400	Flanking Active TSS	HepG2	liver
14	chr1:154325800-154326400	Enhancers	HMEC	breast
15	chr1:154325800-154326600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:154325800-154326600	Enhancers	Colon Smooth Muscle	Colon
17	chr1:154325800-154326600	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr1:154325800-154326600	Bivalent Enhancer	Fetal Thymus	thymus
19	chr1:154325800-154326600	Enhancers	HSMM	muscle
20	chr1:154325800-154326600	Enhancers	HUVEC	blood vessel
21	chr1:154325800-154326800	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:154325800-154326800	Enhancers	Esophagus	oesophagus
23	chr1:154325800-154326800	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr1:154325800-154326800	Enhancers	Ovary	ovary
25	chr1:154325800-154327000	Enhancers	NHLF	lung
26	chr1:154325800-154327200	Enhancers	Primary T cells from cord blood	blood
27	chr1:154325800-154327200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr1:154325800-154327400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:154325800-154327600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:154325800-154327600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr1:154325800-154327600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:154325800-154327600	Enhancers	Placenta	Placenta
33	chr1:154325800-154327800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:154325800-154328400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:154325800-154328400	Enhancers	Stomach Mucosa	stomach
36	chr1:154326000-154326400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:154326000-154326400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:154326000-154326400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:154326000-154326400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:154326000-154326400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:154326000-154326400	Enhancers	Liver	Liver
42	chr1:154326000-154326400	Enhancers	Brain Anterior Caudate	brain
43	chr1:154326000-154326400	Enhancers	Right Atrium	heart
44	chr1:154326000-154326400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr1:154326000-154326600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:154326000-154326600	Enhancers	A549	lung
47	chr1:154326000-154326800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:154326000-154326800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:154326000-154327000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:154326000-154327000	Enhancers	Right Ventricle	heart

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