Variant report

Variant	rs34799808
Chromosome Location	chr1:85745039-85745040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCC1	chr1:85744532-85745314	Hela-S3	cervix:	n/a	n/a
2	JUN	chr1:85744425-85745740	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
3	MAFK	chr1:85744501-85745203	K562	blood:	n/a	chr1:85744729-85744738 chr1:85744729-85744739 chr1:85744742-85744757 chr1:85744689-85744700 chr1:85744618-85744633
4	JUND	chr1:85744329-85745186	HCT-116	colon:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
5	SIN3AK20	chr1:85744479-85745131	HCT-116	colon:	n/a	n/a
6	RXRA	chr1:85744404-85745081	SK-N-SH	brain:	n/a	chr1:85744539-85744552 chr1:85744540-85744551 chr1:85744539-85744552
7	PBX3	chr1:85744331-85745079	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr1:85744699-85745053	Gliobla	brain:	n/a	n/a
9	JUND	chr1:85744322-85745112	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
10	GATA3	chr1:85744342-85745131	SK-N-SH	brain:	n/a	chr1:85744620-85744630 chr1:85744486-85744497 chr1:85744596-85744603
11	SP1	chr1:85744309-85745181	HCT-116	colon:	n/a	chr1:85744679-85744700
12	MTA3	chr1:85744502-85745040	GM12878	blood:	n/a	n/a
13	TCF12	chr1:85744438-85745122	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr1:85744313-85745100	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr1:85744386-85745051	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr1:85744509-85745361	GM12892	blood:	n/a	n/a
17	MAX	chr1:85744394-85745107	A549	lung:	n/a	n/a
18	FOSL1	chr1:85744325-85745062	HCT-116	colon:	n/a	chr1:85744729-85744740 chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
19	FOSL1	chr1:85744351-85745217	HCT-116	colon:	n/a	chr1:85744729-85744740 chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
20	JUND	chr1:85744309-85745294	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
21	RUNX3	chr1:85744525-85745057	GM12878	blood:	n/a	n/a
22	JUND	chr1:85744324-85745112	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
23	KAP1	chr1:85744469-85745162	U2OS	brain:	n/a	n/a
24	SP1	chr1:85744385-85745215	HCT-116	colon:	n/a	chr1:85744679-85744700
25	FOSL2	chr1:85744395-85745095	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
26	PML	chr1:85744426-85745090	K562	blood:	n/a	n/a
27	POLR2A	chr1:85744278-85745155	U87	brain:	n/a	n/a
28	CUX1	chr1:85744389-85745107	K562	blood:	n/a	n/a
29	PBX3	chr1:85744399-85745058	SK-N-SH	brain:	n/a	n/a
30	MAX	chr1:85744425-85745040	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:85744612-85745085	K562	blood:	n/a	n/a
32	SIN3AK20	chr1:85744318-85745121	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:85744412-85745161	U87	brain:	n/a	n/a
34	POLR2A	chr1:85744424-85745162	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:85744335-85745541	HUVEC	blood vessel:	n/a	n/a
36	GATA3	chr1:85744393-85745190	SK-N-SH	brain:	n/a	chr1:85744620-85744630 chr1:85744486-85744497 chr1:85744596-85744603
37	PRDM1	chr1:85744572-85745041	Hela-S3	cervix:	n/a	chr1:85744819-85744834
38	POLR2A	chr1:85744461-85745056	MCF10A-Er-Src	breast:	n/a	n/a
39	EP300	chr1:85744321-85745072	SK-N-SH	brain:	n/a	n/a
40	JUND	chr1:85744318-85745124	HCT-116	colon:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
41	BHLHE40	chr1:85744459-85745039	K562	blood:	n/a	n/a
42	ATF2	chr1:85744436-85745039	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:85744396-85745039	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85744913..85746846-chr1:85930995..85932650,2	MCF-7	breast:
2	chr1:85744748..85747168-chr1:85749238..85751854,3	MCF-7	breast:
3	chr1:85743465..85746291-chr1:85746776..85749038,2	MCF-7	breast:
4	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:
5	chr1:85739297..85743309-chr1:85744628..85748559,4	MCF-7	breast:

Variant related genes	Relation type
BCL10	TF binding region
ENSG00000142871	Chromatin interaction
ENSG00000264380	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000223653	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11802390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802530	1.00[AMR][1000 genomes]
rs11802673	1.00[AMR][1000 genomes]
rs11806417	1.00[AMR][1000 genomes]
rs11808537	1.00[AMR][1000 genomes]
rs11809702	1.00[AMR][1000 genomes]
rs11809826	1.00[AMR][1000 genomes]
rs11809833	1.00[AMR][1000 genomes]
rs11811123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs233070	1.00[AMR][1000 genomes]
rs34609757	1.00[AMR][1000 genomes]
rs36069698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742800-85763000	Weak transcription	Ovary	ovary
2	chr1:85743000-85745400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85743000-85746000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:85743000-85747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:85743000-85749200	Weak transcription	Fetal Stomach	stomach
6	chr1:85743000-85749200	Weak transcription	Psoas Muscle	Psoas
7	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
8	chr1:85743200-85745200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:85743200-85745200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:85743200-85745200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:85743200-85745800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:85743200-85747800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:85743200-85747800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:85743200-85747800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:85743200-85748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:85743200-85748200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:85743200-85752000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:85743400-85748000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:85743400-85748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:85744000-85745800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:85744200-85745400	Enhancers	Fetal Intestine Small	intestine
22	chr1:85744400-85745200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:85744400-85745200	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:85744400-85745200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:85744400-85745200	Flanking Active TSS	GM12878-XiMat	blood
26	chr1:85744400-85745200	Flanking Active TSS	Osteobl	bone
27	chr1:85744400-85745400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:85744400-85745400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:85744400-85745400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:85744400-85745400	Enhancers	Fetal Intestine Large	intestine
31	chr1:85744400-85745400	Enhancers	Small Intestine	intestine
32	chr1:85744400-85745400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:85744400-85745600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:85744400-85745600	Enhancers	Stomach Mucosa	stomach
35	chr1:85744600-85745200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:85744600-85745200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:85744600-85745200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr1:85744600-85745200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:85744600-85745200	Enhancers	Fetal Kidney	kidney
40	chr1:85744600-85745200	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:85744600-85745200	Flanking Active TSS	A549	lung
42	chr1:85744600-85745200	Flanking Active TSS	Hela-S3	cervix
43	chr1:85744600-85745200	Flanking Active TSS	HUVEC	blood vessel
44	chr1:85744600-85745200	Flanking Active TSS	K562	blood
45	chr1:85744600-85745400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:85744600-85745400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:85744600-85745400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:85744600-85745400	Flanking Active TSS	HSMM	muscle
49	chr1:85744600-85745600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:85744600-85745600	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links