Variant report

Variant	rs1546841
Chromosome Location	chr7:100855823-100855824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:100855745-100855863	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:100847341-100856339	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:100845614..100849082-chr7:100852501..100856274,3	K562	blood:
2	chr7:100846805..100850556-chr7:100852421..100856995,5	K562	blood:
3	chr7:100807035..100811166-chr7:100854328..100856818,4	MCF-7	breast:
4	chr7:100847669..100852607-chr7:100855025..100859313,4	MCF-7	breast:
5	chr7:100853413..100857189-chr7:100859048..100862216,5	K562	blood:
6	chr7:100854110..100856306-chr7:100888195..100889806,2	MCF-7	breast:
7	chr7:100850699..100858131-chr7:100858977..100863722,10	K562	blood:
8	chr7:100853184..100857478-chr7:100859517..100863375,8	MCF-7	breast:

No data

Variant related genes	Relation type
PLOD3	TF binding region
ENSG00000106400	Chromatin interaction
ENSG00000128564	Chromatin interaction
ENSG00000214253	Chromatin interaction
ENSG00000213394	Chromatin interaction
ENSG00000205267	Chromatin interaction
ENSG00000106397	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10215699	0.90[ASN][1000 genomes]
rs10487887	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs11546151	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11971003	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11973058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11973909	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11975104	1.00[ASN][1000 genomes]
rs11975752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11977763	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1546840	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1546842	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1811203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1811204	1.00[ASN][1000 genomes]
rs1972170	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2107803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2286120	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2301904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3779113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3779114	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs917112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs926156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv1018841	chr7:100760410-100868299	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv534186	chr7:100773842-100898909	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv607973	chr7:100782460-100873835	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv888816	chr7:100792810-100862264	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv464651	chr7:100792810-100971604	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv607974	chr7:100792810-100971604	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	esv2752134	chr7:100800131-101141867	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv607975	chr7:100804140-100873835	Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv464652	chr7:100804140-100881640	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv607976	chr7:100804140-100881640	Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv888817	chr7:100804140-100881640	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv607977	chr7:100818846-100881640	Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv831076	chr7:100828847-101011674	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription 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	37 gene(s)	inside rSNPs	diseases
19	nsv888818	chr7:100833153-100895480	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
20	nsv888819	chr7:100833153-100920007	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
21	esv2422326	chr7:100833449-101000131	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1546841	PLOD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100844600-100856800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:100844600-100859000	Weak transcription	Hela-S3	cervix
3	chr7:100845800-100859600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:100846600-100858200	Weak transcription	NHDF-Ad	bronchial
5	chr7:100847000-100858000	Weak transcription	HepG2	liver
6	chr7:100847000-100858200	Weak transcription	GM12878-XiMat	blood
7	chr7:100847000-100859400	Weak transcription	HSMM	muscle
8	chr7:100847000-100859800	Weak transcription	Primary B cells from cord blood	blood
9	chr7:100847000-100859800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:100847600-100859400	Weak transcription	Stomach Mucosa	stomach
11	chr7:100847800-100858200	Weak transcription	K562	blood
12	chr7:100847800-100859600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:100847800-100859800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:100848000-100858200	Weak transcription	NH-A	brain
15	chr7:100848200-100859400	Strong transcription	Fetal Intestine Small	intestine
16	chr7:100848600-100859400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:100848800-100856800	Strong transcription	Fetal Brain Female	brain
18	chr7:100848800-100859400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:100848800-100859400	Strong transcription	Fetal Stomach	stomach
20	chr7:100849000-100856000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr7:100849000-100857000	Strong transcription	Right Ventricle	heart
22	chr7:100849000-100858000	Strong transcription	Fetal Muscle Leg	muscle
23	chr7:100849000-100858000	Strong transcription	Ovary	ovary
24	chr7:100849000-100858200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:100849000-100858200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:100849000-100858400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:100849000-100859400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:100849200-100856600	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr7:100849200-100856600	Strong transcription	Brain Germinal Matrix	brain
30	chr7:100849200-100856800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr7:100849200-100857000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:100849200-100857200	Strong transcription	Liver	Liver
33	chr7:100849200-100857800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:100849200-100858200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:100849200-100858200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr7:100849200-100858400	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr7:100849200-100859000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr7:100849200-100859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:100849200-100859000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:100849200-100859000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:100849200-100859200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:100849200-100859200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:100849200-100859200	Strong transcription	Spleen	Spleen
44	chr7:100849200-100859400	Strong transcription	Adipose Nuclei	Adipose
45	chr7:100849200-100859400	Strong transcription	Brain Hippocampus Middle	brain
46	chr7:100849200-100859400	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr7:100849400-100856600	Strong transcription	Placenta	Placenta
48	chr7:100849400-100857000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr7:100849400-100857200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:100849400-100857200	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links