Variant report

Variant	rs560818323
Chromosome Location	chr1:209944253-209944254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 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	STAT5A	chr1:209943577-209945094	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:209941537-209945106	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:209941560-209945629	GM12878	blood:	n/a	n/a
6	POU2F2	chr1:209943526-209944502	GM12878	blood:	n/a	n/a
7	CTCF	chr1:209943655-209945439	GM19239	blood:	n/a	n/a
8	POLR2A	chr1:209943562-209945093	HL-60	blood:	n/a	n/a
9	POLR2A	chr1:209941574-209945063	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:209941567-209945023	GM18526	blood:	n/a	n/a
11	POLR2A	chr1:209943512-209945521	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:209943950-209944460	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:209941117-209946709	GM18505	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	chr1:209941509-209947286	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:209943536-209945521	GM12891	blood:	n/a	n/a
18	POLR2A	chr1:209941597-209945746	GM19099	blood:	n/a	n/a
19	POLR2A	chr1:209941520-209945190	GM15510	blood:	n/a	n/a
20	NR2C2	chr1:209943704-209945090	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:209942360-209945616	GM12892	blood:	n/a	n/a
22	MYC	chr1:209944046-209944277	MCF-7	breast:	n/a	n/a
23	ZEB1	chr1:209943163-209945525	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:209943578-209945455	GM12891	blood:	n/a	n/a
25	STAT5A	chr1:209942515-209946308	GM12878	blood:	n/a	chr1:209942981-209942989 chr1:209942982-209942994 chr1:209945841-209945853 chr1:209943537-209943545
26	POLR2A	chr1:209942422-209945671	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:209943659-209945080	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:209943517-209945479	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:209944234-209944284	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:209943573-209945492	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:209943578-209944728	GM12891	blood:	n/a	n/a
32	ZEB1	chr1:209943523-209945114	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	chr1:209943015..209945017-chr1:209946674..209949825,3	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-4	chr1:209944227-209944789	NONHSAT009236
2	lnc-HSD11B1-4	chr1:209944247-209945468	NONHSAT009238
3	lnc-HSD11B1-4	chr1:209944247-209945468	NONHSAT009240
4	lnc-HSD11B1-4	chr1:209944201-209944669	NONHSAT009242

No data

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv3357365	chr1:209943809-209944578	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:86 , 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	chr1:209941400-209944400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr1:209941400-209945000	Flanking Active TSS	GM12878-XiMat	blood
5	chr1:209941600-209944400	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr1:209941600-209944400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:209941800-209944600	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr1:209941800-209944800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:209941800-209945000	Enhancers	Left Ventricle	heart
10	chr1:209942000-209944800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:209942000-209944800	Enhancers	Brain Substantia Nigra	brain
12	chr1:209942000-209945400	Enhancers	Placenta	Placenta
13	chr1:209942400-209944600	Flanking Active TSS	Fetal Thymus	thymus
14	chr1:209942800-209944600	Enhancers	Fetal Muscle Trunk	muscle
15	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
16	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:209943000-209944400	Enhancers	Right Atrium	heart
18	chr1:209943200-209944600	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr1:209943200-209944800	Enhancers	Colon Smooth Muscle	Colon
20	chr1:209943200-209944800	Enhancers	Right Ventricle	heart
21	chr1:209943200-209945000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:209943200-209945000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:209943200-209945400	Enhancers	Lung	lung
24	chr1:209943200-209945600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr1:209943200-209950600	Weak transcription	Psoas Muscle	Psoas
26	chr1:209943400-209944400	Weak transcription	Brain Angular Gyrus	brain
27	chr1:209943400-209944600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:209943400-209945000	Enhancers	Adipose Nuclei	Adipose
29	chr1:209943400-209945400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:209943400-209952600	Weak transcription	Fetal Intestine Small	intestine
31	chr1:209943600-209944600	Transcr. at gene 5' and 3'	Thymus	Thymus
32	chr1:209943600-209944800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:209943600-209945000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr1:209943600-209945000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:209943600-209945600	Enhancers	Primary hematopoietic stem cells	blood
36	chr1:209943600-209945600	Enhancers	Gastric	stomach
37	chr1:209943600-209945800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:209943600-209951000	Weak transcription	HSMMtube	muscle
39	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:209943800-209944600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:209943800-209944600	Genic enhancers	Pancreas	Pancrea
42	chr1:209943800-209944800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr1:209943800-209945000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr1:209943800-209945000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:209943800-209945000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr1:209943800-209945000	Enhancers	Liver	Liver
47	chr1:209943800-209945000	ZNF genes & repeats	Fetal Kidney	kidney
48	chr1:209943800-209945400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:209943800-209945600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr1:209943800-209945600	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links