Variant report

Variant	rs688659
Chromosome Location	chr1:241801595-241801596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:241800664-241801619	K562	blood:	n/a	n/a
2	KAP1	chr1:241800617-241801819	HEK293	kidney:	n/a	n/a
3	MYC	chr1:241800873-241801914	K562	blood:	n/a	n/a
4	GABPA	chr1:241801350-241801839	A549	lung:	n/a	n/a
5	RFX5	chr1:241801561-241802852	Hela-S3	cervix:	n/a	n/a
6	GABPA	chr1:241801364-241801769	A549	lung:	n/a	n/a
7	ELF1	chr1:241800988-241801692	K562	blood:	n/a	n/a
8	POLR2A	chr1:241801564-241801713	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:241800423-241802084	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:241800646-241801982	Hela-S3	cervix:	n/a	n/a
11	RCOR1	chr1:241800704-241801774	K562	blood:	n/a	n/a
12	RCOR1	chr1:241800549-241801766	Hela-S3	cervix:	n/a	n/a
13	E2F4	chr1:241801591-241801877	MCF10A-Er-Src	breast:	n/a	n/a
14	USF2	chr1:241800721-241801810	Hela-S3	cervix:	n/a	n/a
15	MAX	chr1:241800882-241801797	Hela-S3	cervix:	n/a	n/a
16	GTF2F1	chr1:241800776-241801945	Hela-S3	cervix:	n/a	n/a
17	SPI1	chr1:241801497-241801845	HL-60	blood:	n/a	chr1:241801572-241801585
18	SPI1	chr1:241801475-241801707	K562	blood:	n/a	chr1:241801572-241801585
19	POLR2A	chr1:241799353-241805428	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:241801309..241803243-chr1:241980186..241981798,2	MCF-7	breast:
2	chr1:241800930..241802917-chr1:241824611..241827597,2	K562	blood:
3	chr1:241800110..241802719-chr1:241917456..241919841,2	K562	blood:
4	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
5	chr1:241800780..241802686-chr1:241902251..241905024,2	MCF-7	breast:
6	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
7	chr1:241801200..241805205-chr1:241910998..241914529,7	MCF-7	breast:
8	chr1:241800601..241802586-chr1:241998069..242000945,2	MCF-7	breast:
9	chr1:241800797..241802714-chr1:241839800..241842024,2	K562	blood:
10	chr1:241800150..241802189-chr1:241935454..241937787,2	MCF-7	breast:
11	chr1:241797614..241799339-chr1:241801296..241804255,2	MCF-7	breast:
12	chr1:241799429..241802453-chr1:241804405..241808572,4	MCF-7	breast:
13	chr1:241800454..241803347-chr1:241897717..241900787,4	K562	blood:
14	chr1:241800887..241803348-chr1:241881120..241884579,4	K562	blood:
15	chr1:241801013..241803441-chr1:241985272..241988117,2	K562	blood:
16	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
17	chr1:241801132..241803391-chr1:241936731..241938853,2	K562	blood:
18	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
19	chr1:241678718..241680701-chr1:241800665..241802574,2	K562	blood:
20	chr1:241800930..241803324-chr1:241824611..241827531,2	K562	blood:

No data

Variant related genes	Relation type
CHML	TF binding region
ENSG00000203668	Chromatin interaction
ENSG00000162843	Chromatin interaction
ENSG00000117009	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2756224	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765821	0.91[JPT][hapmap]
rs584695	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs587640	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593963	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs614251	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs622726	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624385	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628720	0.91[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs631143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652571	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676750	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684338	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513451	0.82[EUR][1000 genomes]
rs7513575	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs688659	CHML	cis	cerebellum	SCAN
rs688659	OPN3	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
2	chr1:241787800-241802400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:241788200-241802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:241788200-241802800	Weak transcription	Esophagus	oesophagus
5	chr1:241789200-241802800	Weak transcription	Pancreas	Pancrea
6	chr1:241791600-241802200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:241791600-241802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:241791600-241802400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:241791800-241801800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:241791800-241802200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:241791800-241802400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:241797200-241802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:241798800-241802200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:241798800-241802400	Weak transcription	Lung	lung
15	chr1:241799200-241802200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:241799600-241802200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:241799600-241802400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:241799600-241802400	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:241799600-241804400	Active TSS	Brain Angular Gyrus	brain
20	chr1:241799800-241801600	Enhancers	HepG2	liver
21	chr1:241799800-241802000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:241799800-241802200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:241799800-241802400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:241800200-241801600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:241800200-241801600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:241800200-241801600	Enhancers	Fetal Kidney	kidney
27	chr1:241800200-241801800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:241800200-241801800	Flanking Active TSS	Hela-S3	cervix
29	chr1:241800200-241802000	Flanking Active TSS	HMEC	breast
30	chr1:241800200-241802200	Enhancers	Fetal Thymus	thymus
31	chr1:241800200-241802400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:241800400-241801600	Enhancers	Brain Germinal Matrix	brain
33	chr1:241800400-241801600	Enhancers	Fetal Lung	lung
34	chr1:241800400-241801600	Transcr. at gene 5' and 3'	A549	lung
35	chr1:241800400-241801800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:241800400-241802000	Enhancers	Primary hematopoietic stem cells	blood
37	chr1:241800400-241802000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:241800400-241802000	Flanking Active TSS	NHEK	skin
39	chr1:241800400-241802200	Enhancers	Psoas Muscle	Psoas
40	chr1:241800400-241802200	Enhancers	Osteobl	bone
41	chr1:241800400-241802400	Enhancers	Colon Smooth Muscle	Colon
42	chr1:241800400-241802800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:241800400-241804200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:241800600-241801600	Enhancers	Aorta	Aorta
45	chr1:241800600-241801600	Enhancers	Fetal Brain Male	brain
46	chr1:241800600-241801800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:241800600-241801800	Enhancers	Fetal Heart	heart
48	chr1:241800600-241801800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:241800600-241802000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:241800600-241802200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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