Variant report

Variant	rs17249561
Chromosome Location	chr6:24664930-24664931
allele	C/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	chr6:24662292-24665727	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24645025..24646837-chr6:24661272..24665022,3	MCF-7	breast:
2	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
3	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:

Variant related genes	Relation type
ACOT13	TF binding region
ENSG00000112308	Chromatin interaction
ENSG00000137261	Chromatin interaction

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

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

rs_ID	r²[population]
rs11559067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889567	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17243136	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17243276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17412874	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17419844	1.00[ASN][1000 genomes]
rs17491730	1.00[ASN][1000 genomes]
rs3212238	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400556	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400558	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400559	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400760	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400773	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400774	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400783	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400789	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62400790	1.00[ASN][1000 genomes]
rs62400791	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62400792	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62400793	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62400795	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62400819	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62400821	0.80[AMR][1000 genomes]
rs62400822	0.80[AMR][1000 genomes]
rs62402860	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62402863	0.92[EUR][1000 genomes]
rs62402864	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24646800-24666000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:24647000-24666400	Weak transcription	Esophagus	oesophagus
3	chr6:24649400-24665200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:24650000-24665000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:24653800-24666200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:24654000-24665200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:24654200-24665000	Weak transcription	Brain Substantia Nigra	brain
8	chr6:24654200-24665000	Weak transcription	Fetal Lung	lung
9	chr6:24654400-24665200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:24655400-24665000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:24656200-24665000	Weak transcription	Fetal Heart	heart
12	chr6:24656200-24666000	Weak transcription	Aorta	Aorta
13	chr6:24657400-24665400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:24658400-24665600	Strong transcription	HSMM	muscle
15	chr6:24659000-24665000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:24660000-24665400	Weak transcription	NHDF-Ad	bronchial
17	chr6:24660200-24665600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:24660400-24665000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:24660400-24665200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:24660600-24666200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:24660800-24665000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:24660800-24665000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:24661000-24665000	Strong transcription	K562	blood
24	chr6:24661200-24665000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr6:24661200-24665000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr6:24661600-24665000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:24661600-24665600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr6:24662000-24665000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:24662200-24665000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr6:24662200-24665000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr6:24662200-24665000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:24662200-24665000	Genic enhancers	Brain Hippocampus Middle	brain
33	chr6:24662200-24665000	Strong transcription	Fetal Stomach	stomach
34	chr6:24662200-24665400	Strong transcription	Fetal Muscle Leg	muscle
35	chr6:24662400-24665000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:24662600-24665400	Weak transcription	Right Atrium	heart
37	chr6:24662600-24666400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:24662800-24665000	Genic enhancers	Brain Germinal Matrix	brain
39	chr6:24662800-24665200	Weak transcription	Stomach Mucosa	stomach
40	chr6:24662800-24665200	Strong transcription	NHEK	skin
41	chr6:24662800-24665400	Strong transcription	Osteobl	bone
42	chr6:24662800-24665800	Transcr. at gene 5' and 3'	A549	lung
43	chr6:24663000-24666200	Weak transcription	Pancreas	Pancrea
44	chr6:24663200-24665000	Genic enhancers	Hela-S3	cervix
45	chr6:24663200-24665200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr6:24663200-24665200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
47	chr6:24663400-24665200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:24663600-24665200	Genic enhancers	Dnd41	blood
49	chr6:24663600-24665600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr6:24663600-24666200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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