Variant report

Variant	rs6669714
Chromosome Location	chr1:247498567-247498568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:247498195-247499259	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:247498480-247498773	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr1:247494422-247505513	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:247498559-247498955	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:247497876-247498616	SK-N-MC	brain:	n/a	n/a
6	GATA2	chr1:247497768-247499004	SH-SY5Y	brain:	n/a	chr1:247498753-247498764 chr1:247498742-247498759
7	POLR2A	chr1:247497555-247498603	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:247494396-247499332	K562	blood:	n/a	n/a
9	POLR2A	chr1:247497823-247499466	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:247494236-247499105	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr1:247497775-247498693	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:247494209-247500059	K562	blood:	n/a	n/a
13	POLR2A	chr1:247497751-247499213	K562	blood:	n/a	n/a
14	POLR2A	chr1:247494445-247501569	K562	blood:	n/a	n/a
15	POLR2A	chr1:247498108-247498574	GM12891	blood:	n/a	n/a
16	POLR2A	chr1:247494301-247499306	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:247498456-247498717	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:247493567-247500327	K562	blood:	n/a	n/a
19	POLR2A	chr1:247494315-247499248	K562	blood:	n/a	n/a
20	POLR2A	chr1:247494342-247501582	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:247494334-247499143	K562	blood:	n/a	n/a
22	POLR2A	chr1:247494333-247499244	K562	blood:	n/a	n/a
23	POLR2A	chr1:247495093-247499947	K562	blood:	n/a	n/a
24	POLR2A	chr1:247493627-247501497	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:247493863-247500190	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247450966..247454008-chr1:247495973..247498678,3	K562	blood:
2	chr1:247490651..247493187-chr1:247497913..247500341,2	MCF-7	breast:
3	chr1:247497896..247501644-chr1:247501987..247504336,4	MCF-7	breast:
4	chr1:247089398..247090999-chr1:247497289..247500045,2	K562	blood:
5	chr1:247342736..247346262-chr1:247495942..247498816,3	K562	blood:
6	chr1:247496074..247498986-chr1:247563500..247566011,2	K562	blood:
7	chr1:247497043..247499378-chr1:247507440..247508988,2	MCF-7	breast:
8	chr1:247497133..247499092-chr1:249129196..249131643,2	K562	blood:
9	chr1:247497499..247499211-chr1:247511001..247512771,2	MCF-7	breast:
10	chr1:247374235..247377046-chr1:247498080..247500631,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRP3-1	chr1:247495187-247498708	NONHSAT010771

No data

Variant related genes	Relation type
ZNF496	TF binding region
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1057996	1.00[EUR][1000 genomes]
rs10737800	1.00[ASN][1000 genomes]
rs10924980	0.92[EUR][1000 genomes]
rs10924984	1.00[EUR][1000 genomes]
rs1192835	1.00[EUR][1000 genomes]
rs1192836	1.00[EUR][1000 genomes]
rs12239714	0.82[EUR][1000 genomes]
rs16846406	1.00[EUR][1000 genomes]
rs1771919	1.00[EUR][1000 genomes]
rs1771928	1.00[EUR][1000 genomes]
rs1771944	0.84[EUR][1000 genomes]
rs1771945	1.00[EUR][1000 genomes]
rs1771946	1.00[EUR][1000 genomes]
rs1778548	1.00[EUR][1000 genomes]
rs1891074	1.00[EUR][1000 genomes]
rs2793288	1.00[EUR][1000 genomes]
rs2799179	0.84[EUR][1000 genomes]
rs4925535	1.00[EUR][1000 genomes]
rs56322743	1.00[EUR][1000 genomes]
rs57178323	1.00[EUR][1000 genomes]
rs61276550	1.00[EUR][1000 genomes]
rs6657577	1.00[EUR][1000 genomes]
rs6671690	1.00[EUR][1000 genomes]
rs6676056	1.00[EUR][1000 genomes]
rs6689651	1.00[EUR][1000 genomes]
rs74152973	0.91[EUR][1000 genomes]
rs74152980	1.00[EUR][1000 genomes]
rs74152988	1.00[EUR][1000 genomes]
rs74152993	1.00[EUR][1000 genomes]
rs7517006	0.92[EUR][1000 genomes]
rs7556185	1.00[ASN][1000 genomes]
rs947174	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
6	esv1799864	chr1:247494789-247500650	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247496200-247503000	Weak transcription	Aorta	Aorta
2	chr1:247496400-247498600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:247496400-247499200	Enhancers	Spleen	Spleen
4	chr1:247496400-247501600	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:247496400-247511000	Weak transcription	Primary B cells from cord blood	blood
6	chr1:247496600-247498800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:247496600-247499000	Enhancers	Right Ventricle	heart
8	chr1:247496600-247499200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:247496600-247499200	Enhancers	Fetal Lung	lung
10	chr1:247496600-247499200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
11	chr1:247496600-247499200	Enhancers	Left Ventricle	heart
12	chr1:247496600-247500400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:247496600-247501000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:247496600-247501000	Weak transcription	NHDF-Ad	bronchial
15	chr1:247496600-247505800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:247496600-247506000	Weak transcription	HSMMtube	muscle
17	chr1:247496600-247511000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:247496800-247498600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:247496800-247498800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:247496800-247498800	Enhancers	Pancreas	Pancrea
21	chr1:247496800-247499000	Weak transcription	HUVEC	blood vessel
22	chr1:247496800-247500400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:247496800-247500800	Weak transcription	Ovary	ovary
24	chr1:247496800-247501200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:247496800-247501200	Genic enhancers	Fetal Muscle Leg	muscle
26	chr1:247496800-247501400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:247496800-247502000	Weak transcription	HSMM	muscle
28	chr1:247496800-247502200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:247496800-247503000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:247496800-247507200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:247496800-247510200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:247497000-247498800	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr1:247497000-247499200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:247497000-247499600	Enhancers	Brain Germinal Matrix	brain
35	chr1:247497000-247500000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:247497000-247501600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:247497000-247503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:247497000-247504000	Weak transcription	Stomach Mucosa	stomach
39	chr1:247497000-247511200	Weak transcription	Esophagus	oesophagus
40	chr1:247497200-247498800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:247497200-247499000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:247497200-247499000	Strong transcription	Fetal Stomach	stomach
43	chr1:247497200-247499200	Enhancers	H9 Cell Line	embryonic stem cell
44	chr1:247497200-247499600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:247497200-247499600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:247497200-247500800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr1:247497200-247500800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:247497200-247502200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:247497200-247503000	Weak transcription	NHEK	skin
50	chr1:247497200-247505800	Weak transcription	Brain Substantia Nigra	brain

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