Variant report

Variant	rs73093328
Chromosome Location	chr1:227937973-227937974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr1:227937968-227938323	K562	blood:	n/a	n/a
2	POLR2A	chr1:227934449-227938226	PBDE	blood:	n/a	n/a
3	MAX	chr1:227937947-227938247	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227913557..227915723-chr1:227936561..227939351,2	K562	blood:
2	chr1:227923199..227926110-chr1:227936380..227938690,2	K562	blood:
3	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
4	chr1:227933014..227936120-chr1:227936917..227939887,3	K562	blood:
5	chr1:227936020..227939973-chr1:227940260..227944026,6	K562	blood:
6	chr1:227921065..227923056-chr1:227937528..227939336,2	MCF-7	breast:
7	chr1:227913817..227915723-chr1:227936510..227938061,2	K562	blood:

No data

Variant related genes	Relation type
SNAP47-AS1	TF binding region
ENSG00000230005	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12563564	1.00[AMR][1000 genomes]
rs12564917	1.00[AMR][1000 genomes]
rs12565618	1.00[AMR][1000 genomes]
rs12565653	1.00[AMR][1000 genomes]
rs12567084	1.00[AMR][1000 genomes]
rs16847987	1.00[AMR][1000 genomes]
rs17492447	1.00[AMR][1000 genomes]
rs2101862	1.00[AMR][1000 genomes]
rs2313220	1.00[AMR][1000 genomes]
rs35703429	1.00[AMR][1000 genomes]
rs57165550	1.00[AMR][1000 genomes]
rs58322371	1.00[AMR][1000 genomes]
rs59404931	1.00[AMR][1000 genomes]
rs59772630	1.00[AMR][1000 genomes]
rs60835672	1.00[AMR][1000 genomes]
rs61283390	1.00[AMR][1000 genomes]
rs6665512	1.00[AMR][1000 genomes]
rs6675470	1.00[AMR][1000 genomes]
rs73090952	1.00[AMR][1000 genomes]
rs73090959	1.00[AMR][1000 genomes]
rs73090985	1.00[AMR][1000 genomes]
rs73090986	1.00[AMR][1000 genomes]
rs73090987	1.00[AMR][1000 genomes]
rs73090994	1.00[AMR][1000 genomes]
rs73090995	1.00[AMR][1000 genomes]
rs73091000	1.00[AMR][1000 genomes]
rs73092604	1.00[AMR][1000 genomes]
rs73092607	1.00[AMR][1000 genomes]
rs73092610	1.00[AMR][1000 genomes]
rs73092646	1.00[AMR][1000 genomes]
rs73092653	1.00[AMR][1000 genomes]
rs73092661	1.00[AMR][1000 genomes]
rs73092665	1.00[AMR][1000 genomes]
rs73093304	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093319	1.00[AMR][1000 genomes]
rs73093344	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093354	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094528	1.00[AMR][1000 genomes]
rs73094536	1.00[AMR][1000 genomes]
rs73094538	1.00[AMR][1000 genomes]
rs73094556	1.00[AMR][1000 genomes]
rs73094558	1.00[AMR][1000 genomes]
rs73094561	1.00[AMR][1000 genomes]
rs73094571	1.00[AMR][1000 genomes]
rs73098926	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73098933	1.00[AMR][1000 genomes]
rs73099300	1.00[AMR][1000 genomes]
rs73099302	1.00[AMR][1000 genomes]
rs73101625	1.00[AMR][1000 genomes]
rs73101653	1.00[AMR][1000 genomes]
rs7526436	1.00[AMR][1000 genomes]
rs7555208	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227940800	Weak transcription	HSMMtube	muscle
2	chr1:227924200-227941200	Weak transcription	HSMM	muscle
3	chr1:227924200-227941200	Weak transcription	NHDF-Ad	bronchial
4	chr1:227924200-227941600	Weak transcription	Osteobl	bone
5	chr1:227924200-227942000	Weak transcription	Hela-S3	cervix
6	chr1:227924200-227946800	Weak transcription	HUVEC	blood vessel
7	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:227924800-227941400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:227925000-227941400	Weak transcription	Fetal Brain Male	brain
10	chr1:227925200-227941200	Weak transcription	Psoas Muscle	Psoas
11	chr1:227925600-227941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227928600-227941200	Weak transcription	Small Intestine	intestine
13	chr1:227930200-227945600	Weak transcription	NH-A	brain
14	chr1:227930400-227939400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227931800-227938400	Weak transcription	NHEK	skin
16	chr1:227932800-227941400	Weak transcription	Stomach Mucosa	stomach
17	chr1:227932800-227947200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:227933000-227939400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:227933000-227946400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:227933800-227939000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:227934000-227938600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:227934000-227940200	Strong transcription	Thymus	Thymus
23	chr1:227934000-227941400	Strong transcription	Fetal Brain Female	brain
24	chr1:227934000-227948800	Strong transcription	Primary T cells from cord blood	blood
25	chr1:227934200-227945400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:227934400-227938400	Genic enhancers	Fetal Stomach	stomach
27	chr1:227934400-227939600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:227934400-227950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:227934600-227942600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:227934600-227942800	Strong transcription	Brain Germinal Matrix	brain
31	chr1:227934800-227941200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:227934800-227943200	Strong transcription	Fetal Intestine Large	intestine
33	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
35	chr1:227935000-227938000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:227935000-227938800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:227935000-227939200	Genic enhancers	Gastric	stomach
38	chr1:227935000-227939400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:227935000-227939400	Genic enhancers	Right Ventricle	heart
40	chr1:227935000-227939600	Strong transcription	NHLF	lung
41	chr1:227935000-227942600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:227935000-227949600	Strong transcription	Dnd41	blood
43	chr1:227935200-227949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:227935400-227938000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:227935400-227938600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:227935400-227939000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:227935400-227939400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:227935400-227940400	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:227935400-227941800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:227935600-227938000	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links