Variant report

Variant	rs6489321
Chromosome Location	chr12:1799515-1799516
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	MXI1	chr12:1799398-1801752	SK-N-SH	brain:	n/a	n/a
2	JUN	chr12:1799030-1801092	K562	blood:	n/a	chr12:1800125-1800134 chr12:1800811-1800823
3	POLR2A	chr12:1799201-1801657	MCF10A-Er-Src	breast:	n/a	n/a
4	EP300	chr12:1799494-1800020	K562	blood:	n/a	chr12:1799699-1799709
5	E2F6	chr12:1799507-1800405	A549	lung:	n/a	n/a
6	POLR2A	chr12:1799445-1801034	MCF-7	breast:	n/a	n/a
7	SREBP2	chr12:1799376-1801672	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:1799185-1800944	Raji	blood:	n/a	n/a
9	POLR2A	chr12:1799214-1801006	PBDE	blood:	n/a	n/a
10	NFIC	chr12:1799398-1800329	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr12:1799476-1800915	A549	lung:	n/a	chr12:1799900-1799910 chr12:1800352-1800359
12	SREBP1	chr12:1798919-1802146	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:1799240-1801090	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:1799349-1800886	K562	blood:	n/a	n/a
15	HCFC1	chr12:1798998-1801457	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:1799360-1800823	K562	blood:	n/a	n/a
17	MAZ	chr12:1798841-1801165	IMR90	lung:	n/a	chr12:1799900-1799910 chr12:1800352-1800359
18	POLR2A	chr12:1799091-1801940	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:1799219-1799542	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
2	chr12:1769387..1773191-chr12:1797591..1801415,7	K562	blood:
3	chr12:1797794..1800188-chr12:1882818..1885035,2	MCF-7	breast:
4	chr12:1798163..1800510-chr12:1865299..1867613,2	K562	blood:
5	chr12:1768367..1774746-chr12:1797764..1801789,11	MCF-7	breast:

Variant related genes	Relation type
ADIPOR2	TF binding region
ENSG00000266043	Chromatin interaction
ENSG00000243663	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11061904	1.00[EUR][1000 genomes]
rs1860049	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2041059	1.00[EUR][1000 genomes]
rs2108398	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2369974	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2370054	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35510932	1.00[EUR][1000 genomes]
rs4765838	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4766411	1.00[EUR][1000 genomes]
rs4766420	1.00[EUR][1000 genomes]
rs56369812	1.00[EUR][1000 genomes]
rs6489325	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7133749	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7135229	1.00[EUR][1000 genomes]
rs7136278	0.87[AFR][1000 genomes]
rs7297878	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7304843	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7308757	1.00[EUR][1000 genomes]
rs7314133	1.00[EUR][1000 genomes]
rs74061311	1.00[EUR][1000 genomes]
rs74061331	1.00[EUR][1000 genomes]
rs74061332	1.00[EUR][1000 genomes]
rs758026	1.00[EUR][1000 genomes]
rs758027	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs758169	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7957003	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7962777	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7964434	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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 miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1797400-1799600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:1799000-1799600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:1799000-1799600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:1799000-1799600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:1799000-1799600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr12:1799000-1799600	Flanking Active TSS	Dnd41	blood
7	chr12:1799200-1799600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:1799200-1799600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr12:1799200-1799600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:1799200-1799600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:1799200-1799600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:1799200-1799600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr12:1799200-1799600	Enhancers	Primary B cells from cord blood	blood
14	chr12:1799200-1799600	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:1799200-1799600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr12:1799200-1799600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:1799200-1799600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:1799200-1799600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:1799200-1799600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:1799200-1799600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:1799200-1799600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:1799200-1799600	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr12:1799200-1799600	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr12:1799200-1799600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr12:1799200-1799600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:1799200-1799600	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr12:1799200-1799600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr12:1799200-1799600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:1799200-1799600	Enhancers	Thymus	Thymus
30	chr12:1799200-1799600	Flanking Active TSS	A549	lung
31	chr12:1799200-1799600	Flanking Active TSS	GM12878-XiMat	blood
32	chr12:1799200-1799600	Enhancers	HSMM	muscle
33	chr12:1799200-1799600	Flanking Active TSS	HSMMtube	muscle
34	chr12:1799200-1799600	Flanking Active TSS	HUVEC	blood vessel
35	chr12:1799200-1799600	Flanking Active TSS	NH-A	brain
36	chr12:1799200-1799600	Flanking Active TSS	NHLF	lung
37	chr12:1799200-1799800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr12:1799200-1799800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:1799200-1799800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr12:1799200-1799800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr12:1799200-1799800	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr12:1799200-1799800	Flanking Active TSS	Fetal Lung	lung
43	chr12:1799200-1799800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr12:1799200-1799800	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr12:1799200-1799800	Flanking Active TSS	Hela-S3	cervix
46	chr12:1799200-1799800	Flanking Active TSS	HMEC	breast
47	chr12:1799200-1799800	Flanking Active TSS	Osteobl	bone
48	chr12:1799200-1800000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr12:1799200-1800000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:1799200-1800800	Active TSS	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links