Variant report

Variant	rs56746340
Chromosome Location	chr3:51974487-51974488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:51974432-51974551	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
2	chr3:51974226..51977659-chr3:52020694..52024166,4	K562	blood:
3	chr3:51972961..51975805-chr3:51984917..51986970,2	MCF-7	breast:
4	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
5	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
6	chr3:51974263..51977386-chr3:52088681..52091436,3	K562	blood:
7	chr3:51974392..51977854-chr3:52027120..52030701,3	MCF-7	breast:
8	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:

No data

Variant related genes	Relation type
PARP3	TF binding region
ENSG00000090097	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000272762	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs178918	1.00[AMR][1000 genomes]
rs323869	1.00[AMR][1000 genomes]
rs323870	1.00[AMR][1000 genomes]
rs323872	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	1.00[AMR][1000 genomes]
rs323880	1.00[AMR][1000 genomes]
rs323889	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323891	1.00[AMR][1000 genomes]
rs323896	1.00[AMR][1000 genomes]
rs323900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368210	1.00[AMR][1000 genomes]
rs422304	1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961930	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964016	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7426999	1.00[AMR][1000 genomes]
rs7636204	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv590280	chr3:51967439-51978327	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
8	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51965200-51974600	Strong transcription	Fetal Intestine Small	intestine
2	chr3:51966400-51975000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:51966800-51975000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:51968600-51975000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:51970600-51975000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:51971200-51974600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:51971600-51974800	Weak transcription	Fetal Kidney	kidney
8	chr3:51971800-51974600	Weak transcription	Primary B cells from cord blood	blood
9	chr3:51972000-51974600	Weak transcription	NHDF-Ad	bronchial
10	chr3:51972200-51974600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:51972200-51974600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:51972200-51975000	Weak transcription	Left Ventricle	heart
13	chr3:51972200-51975200	Weak transcription	Aorta	Aorta
14	chr3:51972400-51974600	Weak transcription	Psoas Muscle	Psoas
15	chr3:51972400-51974800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:51972400-51975000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:51972600-51974600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:51972600-51974800	Weak transcription	Ovary	ovary
19	chr3:51972800-51975000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:51973000-51974600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:51973000-51974600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:51973000-51974800	Weak transcription	Colonic Mucosa	Colon
23	chr3:51973000-51974800	Weak transcription	Pancreas	Pancrea
24	chr3:51973000-51975400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:51973200-51974600	Enhancers	Adipose Nuclei	Adipose
26	chr3:51973200-51974800	Enhancers	Fetal Brain Female	brain
27	chr3:51973200-51975200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:51973400-51974600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:51973400-51974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:51973400-51974600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:51973400-51974600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:51973400-51974600	Weak transcription	Placenta	Placenta
33	chr3:51973400-51974800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:51973400-51974800	Weak transcription	Primary T cells from cord blood	blood
35	chr3:51973400-51974800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:51973400-51975000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:51973600-51974600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:51973600-51974600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:51973600-51974600	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:51973600-51974600	Weak transcription	Right Ventricle	heart
41	chr3:51973600-51974600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:51973600-51974800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:51973600-51974800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:51973600-51974800	Weak transcription	Brain Anterior Caudate	brain
45	chr3:51973600-51974800	Weak transcription	Fetal Stomach	stomach
46	chr3:51973600-51974800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:51973600-51975000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:51973600-51975000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:51973600-51975000	Weak transcription	Thymus	Thymus
50	chr3:51974000-51974800	Enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links