Variant report

Variant	rs1194597
Chromosome Location	chr1:154237488-154237489
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	chr1:154237247-154237805	GM12891	blood:	n/a	n/a
2	NFATC1	chr1:154237336-154239144	GM12878	blood:	n/a	chr1:154237361-154237375
3	POLR2A	chr1:154232935-154239560	K562	blood:	n/a	n/a
4	POLR2A	chr1:154237249-154237770	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:154237469-154237960	PFSK-1	brain:	n/a	n/a
6	SPI1	chr1:154237345-154237770	HL-60	blood:	n/a	chr1:154237536-154237545 chr1:154237534-154237547 chr1:154237533-154237546
7	POLR2A	chr1:154237463-154237516	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:154237329-154237551	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:154237336-154237960	K562	blood:	n/a	n/a
10	POLR2A	chr1:154236317-154237757	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154166190..154168468-chr1:154235593..154238301,2	K562	blood:
2	chr1:154228115..154231882-chr1:154235436..154238955,4	MCF-7	breast:
3	chr1:154236442..154241812-chr1:154243586..154247600,7	MCF-7	breast:
4	chr1:154189134..154191972-chr1:154235587..154237500,3	MCF-7	breast:
5	chr1:154227049..154228742-chr1:154236510..154238440,2	MCF-7	breast:

Variant related genes	Relation type
UBAP2L	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1113142	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs11265605	1.00[EUR][1000 genomes]
rs11802893	0.91[YRI][hapmap]
rs1194591	1.00[EUR][1000 genomes]
rs1194594	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs1194601	0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194605	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12026177	0.82[YRI][hapmap]
rs12028949	0.82[YRI][hapmap]
rs1205590	0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835846	0.82[YRI][hapmap]
rs16835852	0.91[YRI][hapmap]
rs16835909	1.00[EUR][1000 genomes]
rs1685625	1.00[EUR][1000 genomes]
rs1685626	1.00[EUR][1000 genomes]
rs1760791	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1817688	1.00[EUR][1000 genomes]
rs2340487	1.00[EUR][1000 genomes]
rs2500222	0.91[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2633434	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs3811455	0.82[YRI][hapmap]
rs3935419	0.82[YRI][hapmap]
rs4393148	1.00[EUR][1000 genomes]
rs4406621	1.00[EUR][1000 genomes]
rs4620534	0.91[YRI][hapmap]
rs4845369	1.00[EUR][1000 genomes]
rs4845632	1.00[EUR][1000 genomes]
rs55649582	1.00[EUR][1000 genomes]
rs55650526	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55664806	1.00[EUR][1000 genomes]
rs55857358	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56752149	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57011078	0.87[AMR][1000 genomes]
rs59310765	1.00[EUR][1000 genomes]
rs59651124	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60506384	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60743909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6427694	1.00[EUR][1000 genomes]
rs6666943	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs715737	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs7527520	1.00[EUR][1000 genomes]
rs7556118	1.00[EUR][1000 genomes]
rs9804125	1.00[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
5	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:154196800-154242600	Strong transcription	A549	lung
7	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
15	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:154197600-154239800	Strong transcription	NHLF	lung
20	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
26	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
27	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:154197800-154239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:154197800-154242000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
32	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:154198000-154243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:154198200-154241000	Strong transcription	Dnd41	blood
36	chr1:154198400-154243000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:154199000-154243600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:154199400-154243600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:154200000-154243800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:154205800-154239200	Strong transcription	NHDF-Ad	bronchial
41	chr1:154211000-154243800	Strong transcription	Fetal Intestine Large	intestine
42	chr1:154212000-154239600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:154212200-154239800	Strong transcription	Liver	Liver
44	chr1:154212800-154240200	Strong transcription	Left Ventricle	heart
45	chr1:154213000-154242800	Strong transcription	Colon Smooth Muscle	Colon
46	chr1:154213200-154239000	Strong transcription	HepG2	liver
47	chr1:154213600-154243800	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:154214000-154239600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr1:154214000-154239600	Strong transcription	HMEC	breast
50	chr1:154214000-154243600	Strong transcription	H9 Cell Line	embryonic stem cell

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