Variant report

Variant	rs334690
Chromosome Location	chr1:61719619-61719620
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	POLR2A	chr1:61719029-61720900	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr1:61718855-61720029	U2OS	brain:	n/a	n/a
3	FOS	chr1:61719128-61719841	MCF10A-Er-Src	breast:	n/a	chr1:61719523-61719533
4	FOS	chr1:61719096-61719707	MCF10A-Er-Src	breast:	n/a	chr1:61719523-61719533
5	FOS	chr1:61719059-61719822	MCF10A-Er-Src	breast:	n/a	chr1:61719523-61719533
6	FOS	chr1:61719102-61719866	MCF10A-Er-Src	breast:	n/a	chr1:61719523-61719533
7	POLR2A	chr1:61719216-61719864	MCF10A-Er-Src	breast:	n/a	n/a
8	NR2F2	chr1:61718576-61719620	K562	blood:	n/a	chr1:61719240-61719255
9	CEBPB	chr1:61719017-61719787	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:61546491..61548608-chr1:61718284..61720951,3	K562	blood:

Variant related genes	Relation type
ENSG00000237853	TF binding region
ENSG00000162599	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11207719	0.82[EUR][1000 genomes]
rs12082781	1.00[YRI][hapmap]
rs162878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121858	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs1977653	0.83[EUR][1000 genomes]
rs2275208	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333136	0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333138	0.82[AMR][1000 genomes]
rs333140	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333142	0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs333143	0.92[JPT][hapmap]
rs333144	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333145	0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs333146	0.92[JPT][hapmap]
rs333147	0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs333148	0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs333150	0.82[AMR][1000 genomes]
rs333160	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333162	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs333164	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333165	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs333166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244151	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684051	0.82[EUR][1000 genomes]
rs72664877	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72664888	0.85[EUR][1000 genomes]
rs72664890	0.85[EUR][1000 genomes]
rs72664891	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61680000-61720200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:61708000-61720400	Weak transcription	Colonic Mucosa	Colon
3	chr1:61710200-61720400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:61714400-61720200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:61715600-61720200	Enhancers	Fetal Heart	heart
6	chr1:61715600-61725200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:61716000-61720400	Enhancers	Colon Smooth Muscle	Colon
8	chr1:61716000-61725600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:61717000-61720000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:61717000-61720400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:61717800-61720200	Enhancers	Brain Substantia Nigra	brain
12	chr1:61718400-61720200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:61718400-61721000	Enhancers	HepG2	liver
14	chr1:61718400-61721200	Enhancers	Liver	Liver
15	chr1:61718600-61720200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:61718600-61720200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:61718600-61720200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:61718600-61720200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:61718600-61720200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr1:61718600-61720200	Enhancers	Fetal Lung	lung
21	chr1:61718600-61720200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:61718600-61720200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:61718600-61720200	Enhancers	HMEC	breast
24	chr1:61718600-61720200	Enhancers	NHEK	skin
25	chr1:61718600-61720400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:61718600-61720400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:61718600-61720400	Enhancers	Brain Angular Gyrus	brain
28	chr1:61718600-61720400	Enhancers	Brain Anterior Caudate	brain
29	chr1:61718600-61720400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:61718600-61720400	Enhancers	Right Ventricle	heart
31	chr1:61718600-61721200	Enhancers	Hela-S3	cervix
32	chr1:61718800-61720200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:61718800-61720200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr1:61718800-61720200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:61718800-61720200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:61718800-61720200	Enhancers	Small Intestine	intestine
37	chr1:61718800-61720400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:61718800-61720400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:61718800-61720400	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:61718800-61720400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:61718800-61720400	Enhancers	Fetal Brain Female	brain
42	chr1:61718800-61720400	Enhancers	Fetal Stomach	stomach
43	chr1:61718800-61720400	Enhancers	NHLF	lung
44	chr1:61718800-61720600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:61718800-61720600	Enhancers	Primary hematopoietic stem cells	blood
46	chr1:61718800-61721200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:61718800-61721600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr1:61718800-61721800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:61719000-61720200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:61719000-61720200	Enhancers	Rectal Mucosa Donor 29	rectum

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