Variant report

Variant	rs3773733
Chromosome Location	chr3:53200664-53200665
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53188104..53190681-chr3:53198828..53201211,3	K562	blood:
2	chr3:53199183..53202732-chr3:53204136..53207026,5	K562	blood:
3	chr3:53194953..53199207-chr3:53199454..53201631,4	K562	blood:
4	chr3:53197947..53200890-chr3:53261082..53263674,2	K562	blood:
5	chr3:53199818..53201927-chr3:53878071..53880681,2	MCF-7	breast:
6	chr3:53195153..53196714-chr3:53199399..53202103,2	K562	blood:
7	chr3:53199690..53202730-chr3:53210054..53211867,3	MCF-7	breast:
8	chr3:53188104..53190681-chr3:53199532..53201211,2	K562	blood:
9	chr3:53150999..53152695-chr3:53199764..53202403,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163931	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11130347	0.81[ASN][1000 genomes]
rs11924565	0.87[ASN][1000 genomes]
rs1483185	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483186	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1483187	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2242305	0.82[ASN][1000 genomes]
rs2306571	1.00[JPT][hapmap]
rs3773724	0.90[ASN][1000 genomes]
rs3773726	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3773727	0.83[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3773729	0.90[JPT][hapmap]
rs3773731	0.88[ASN][1000 genomes]
rs3821689	0.90[JPT][hapmap]
rs57046386	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62254282	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6775022	0.90[ASN][1000 genomes]
rs6778964	0.90[JPT][hapmap]
rs6797662	0.90[ASN][1000 genomes]
rs72537447	0.83[ASN][1000 genomes]
rs7630325	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196400-53202000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:53196400-53210200	Weak transcription	Psoas Muscle	Psoas
3	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
4	chr3:53196600-53204000	Weak transcription	Small Intestine	intestine
5	chr3:53197000-53202000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:53197200-53200800	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:53197200-53201800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:53197200-53205400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:53197400-53200800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:53197400-53200800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:53197400-53202000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:53197400-53202200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:53197400-53203000	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr3:53197400-53207000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:53197600-53201000	Weak transcription	HepG2	liver
17	chr3:53197600-53201800	Enhancers	Stomach Mucosa	stomach
18	chr3:53197600-53202000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:53197600-53204200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:53197600-53206600	Genic enhancers	Fetal Intestine Small	intestine
21	chr3:53197600-53206800	Weak transcription	Primary T cells from cord blood	blood
22	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
23	chr3:53197800-53200800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:53197800-53201000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:53197800-53202800	Enhancers	Brain Anterior Caudate	brain
26	chr3:53197800-53203800	Weak transcription	Thymus	Thymus
27	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:53198000-53201600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:53198000-53201800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:53198000-53206800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:53198200-53200800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:53198600-53202200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:53198800-53201600	Genic enhancers	Fetal Intestine Large	intestine
35	chr3:53198800-53202000	Genic enhancers	Spleen	Spleen
36	chr3:53198800-53202200	Genic enhancers	Rectal Mucosa Donor 31	rectum
37	chr3:53199200-53200800	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
38	chr3:53199200-53201600	Enhancers	Right Ventricle	heart
39	chr3:53199200-53202600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:53199400-53200800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
41	chr3:53199400-53201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:53199400-53201000	Genic enhancers	Pancreas	Pancrea
43	chr3:53199400-53201600	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:53199600-53202400	Enhancers	Brain Hippocampus Middle	brain
45	chr3:53199600-53202400	Strong transcription	NHEK	skin
46	chr3:53199600-53203000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:53199600-53205000	Genic enhancers	Esophagus	oesophagus
48	chr3:53199800-53201000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:53199800-53201200	Enhancers	Right Atrium	heart
50	chr3:53199800-53201400	Enhancers	Duodenum Smooth Muscle	Duodenum

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