Variant report

Variant	rs28767240
Chromosome Location	chr1:209945129-209945130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:209941568-209945214	GM18951	blood:	n/a	n/a
2	POU2F2	chr1:209944640-209945550	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:209941560-209945629	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:209945003-209945443	GM12891	blood:	n/a	n/a
6	MYC	chr1:209945086-209945222	MCF-7	breast:	n/a	n/a
7	MYC	chr1:209944955-209945349	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:209943655-209945439	GM19239	blood:	n/a	n/a
9	POLR2A	chr1:209944334-209945446	MCF-7	breast:	n/a	n/a
10	MYC	chr1:209945106-209945200	MCF-7	breast:	n/a	n/a
11	POLR2A	chr1:209943512-209945521	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:209941117-209946709	GM18505	blood:	n/a	n/a
13	POU2F2	chr1:209944894-209945487	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:209942381-209945631	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:209943616-209945450	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:209944289-209945552	GM12878	blood:	n/a	n/a
17	IRF4	chr1:209944855-209945464	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:209941509-209947286	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:209943536-209945521	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:209941597-209945746	GM19099	blood:	n/a	n/a
21	POLR2A	chr1:209941520-209945190	GM15510	blood:	n/a	n/a
22	POLR2A	chr1:209942360-209945616	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:209944809-209945362	Gliobla	brain:	n/a	n/a
24	ZEB1	chr1:209943163-209945525	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:209943578-209945455	GM12891	blood:	n/a	n/a
26	STAT5A	chr1:209942515-209946308	GM12878	blood:	n/a	chr1:209942981-209942989 chr1:209942982-209942994 chr1:209945841-209945853 chr1:209943537-209943545
27	MYC	chr1:209945022-209945352	MCF-7	breast:	n/a	n/a
28	POLR2A	chr1:209942422-209945671	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:209944836-209945332	A549	lung:	n/a	n/a
30	POU2F2	chr1:209944667-209945455	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:209943517-209945479	GM12892	blood:	n/a	n/a
32	PAX5	chr1:209945056-209945441	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:209943573-209945492	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209944533..209945329-chr11:75062797..75063297,2	NB4	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-4	chr1:209944790-209945471	NONHSAT009237
2	lnc-HSD11B1-4	chr1:209944247-209945468	NONHSAT009238
3	lnc-C1orf74-2	chr1:209944455-209945468	NONHSAT009239
4	lnc-HSD11B1-4	chr1:209944247-209945468	NONHSAT009240
5	lnc-HSD11B1-4	chr1:209944860-209945499	NONHSAT009242

No data

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000137486	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11119340	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11119341	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12131636	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4990735	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3429215	chr1:209942329-209947327	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3449118	chr1:209942529-209946727	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
8	esv3393757	chr1:209943129-209946427	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	esv3375148	chr1:209943179-209945677	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	esv3391985	chr1:209943579-209946077	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	esv3424159	chr1:209944927-209945477	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv3351009	chr1:209945038-209945228	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv3348972	chr1:209945126-209945450	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28767240	TRAF3IP3	cis	Whole Blood	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209940800-209946200	Enhancers	Fetal Stomach	stomach
2	chr1:209941000-209945800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:209942000-209945400	Enhancers	Placenta	Placenta
4	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
5	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:209943200-209945400	Enhancers	Lung	lung
7	chr1:209943200-209945600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr1:209943200-209950600	Weak transcription	Psoas Muscle	Psoas
9	chr1:209943400-209945400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:209943400-209952600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:209943600-209945600	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:209943600-209945600	Enhancers	Gastric	stomach
13	chr1:209943600-209945800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:209943600-209951000	Weak transcription	HSMMtube	muscle
15	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:209943800-209945400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:209943800-209945600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr1:209943800-209945600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr1:209943800-209950800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:209943800-209954600	Weak transcription	NHEK	skin
21	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:209944000-209945800	Enhancers	Fetal Heart	heart
26	chr1:209944000-209946000	Enhancers	Stomach Smooth Muscle	stomach
27	chr1:209944000-209946200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:209944000-209952800	Weak transcription	HMEC	breast
29	chr1:209944000-209956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:209944200-209945200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:209944200-209945200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:209944200-209945800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:209944200-209946400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
35	chr1:209944400-209945800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr1:209944400-209947200	Weak transcription	Right Atrium	heart
37	chr1:209944400-209948800	Genic enhancers	Monocytes-CD14+_RO01746	blood
38	chr1:209944600-209945200	Enhancers	Pancreas	Pancrea
39	chr1:209944600-209946000	Genic enhancers	Fetal Thymus	thymus
40	chr1:209944600-209946400	Genic enhancers	Thymus	Thymus
41	chr1:209944600-209954400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:209944800-209945200	Active TSS	Colonic Mucosa	Colon
43	chr1:209944800-209945400	Weak transcription	K562	blood
44	chr1:209944800-209946000	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr1:209944800-209946200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
46	chr1:209944800-209947800	Genic enhancers	Primary B cells from cord blood	blood
47	chr1:209944800-209950000	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr1:209944800-209951200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:209944800-209955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain

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