Variant report

Variant	rs9824752
Chromosome Location	chr3:46019670-46019671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46017706..46019852-chr3:46035209..46037613,2	K562	blood:
2	chr3:46019151..46021048-chr3:46024338..46027316,2	K562	blood:
3	chr3:46014022..46017742-chr3:46018515..46020350,3	MCF-7	breast:
4	chr3:46019490..46020101-chr3:46029374..46029909,2	MCF-7	breast:
5	chr3:45997101..45998721-chr3:46017987..46020675,2	K562	blood:
6	chr3:45970697..45972556-chr3:46017144..46019977,2	K562	blood:

Variant related genes	Relation type
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12330199	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13315494	1.00[EUR][1000 genomes]
rs13316935	1.00[EUR][1000 genomes]
rs13317076	1.00[EUR][1000 genomes]
rs2234359	1.00[EUR][1000 genomes]
rs28670183	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41395345	1.00[EUR][1000 genomes]
rs6774011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7613756	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637926	1.00[EUR][1000 genomes]
rs9311389	1.00[EUR][1000 genomes]
rs9811093	1.00[EUR][1000 genomes]
rs9814852	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9825221	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9829016	1.00[AMR][1000 genomes]
rs9831791	1.00[EUR][1000 genomes]
rs9833683	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9835366	1.00[EUR][1000 genomes]
rs9838832	1.00[EUR][1000 genomes]
rs9841919	1.00[EUR][1000 genomes]
rs9856418	1.00[EUR][1000 genomes]
rs9858301	1.00[EUR][1000 genomes]
rs9859087	1.00[EUR][1000 genomes]
rs9860381	0.81[AFR][1000 genomes]
rs9865446	0.81[AFR][1000 genomes]
rs9870657	1.00[EUR][1000 genomes]
rs9875356	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9882765	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer 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
3	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription 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	11 gene(s)	inside rSNPs	diseases
5	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
2	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:45996200-46025400	Strong transcription	Liver	Liver
11	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:46002600-46025000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:46002600-46027200	Weak transcription	A549	lung
14	chr3:46007800-46024200	Weak transcription	Fetal Kidney	kidney
15	chr3:46008600-46026400	Strong transcription	Hela-S3	cervix
16	chr3:46009000-46027800	Weak transcription	Fetal Brain Male	brain
17	chr3:46010200-46021000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:46010200-46022600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:46010200-46024200	Strong transcription	Left Ventricle	heart
20	chr3:46010200-46027000	Weak transcription	Fetal Brain Female	brain
21	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:46010600-46020800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:46010800-46022400	Weak transcription	Fetal Heart	heart
25	chr3:46011400-46020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:46012000-46020800	Weak transcription	Ovary	ovary
27	chr3:46013000-46026200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:46013600-46021000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:46013600-46023000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:46013600-46025000	Strong transcription	Fetal Intestine Small	intestine
31	chr3:46013600-46025400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:46013600-46025600	Strong transcription	Fetal Stomach	stomach
33	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
34	chr3:46014000-46019800	Strong transcription	Pancreas	Pancrea
35	chr3:46014000-46022400	Strong transcription	K562	blood
36	chr3:46014000-46025800	Strong transcription	HepG2	liver
37	chr3:46014000-46026400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr3:46014200-46026000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:46014600-46020800	Weak transcription	Small Intestine	intestine
40	chr3:46014800-46020800	Weak transcription	NHEK	skin
41	chr3:46015000-46020000	Weak transcription	HMEC	breast
42	chr3:46015000-46022600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:46015000-46025200	Strong transcription	Placenta	Placenta
44	chr3:46015200-46020200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:46015200-46022600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:46015400-46021400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:46015400-46026400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:46015600-46021800	Strong transcription	NHLF	lung
49	chr3:46015600-46022000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:46015600-46022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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