Variant report

Variant	rs59406133
Chromosome Location	chr17:38496752-38496753
allele	A/T
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	HCFC1	chr17:38496596-38498180	Hela-S3	cervix:	n/a	n/a
2	REST	chr17:38496712-38497848	A549	lung:	n/a	chr17:38497052-38497060
3	RCOR1	chr17:38496696-38496819	K562	blood:	n/a	n/a
4	POLR2A	chr17:38496620-38496768	HUVEC	blood vessel:	n/a	n/a
5	CHD1	chr17:38496449-38502844	IMR90	lung:	n/a	chr17:38502765-38502775 chr17:38500190-38500200
6	POLR2A	chr17:38495745-38498511	MCF-7	breast:	n/a	n/a
7	POLR2A	chr17:38495892-38502181	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38472788..38480698-chr17:38493295..38509406,39	K562	blood:
2	chr17:38464338..38472007-chr17:38495904..38503617,17	K562	blood:
3	chr17:38287645..38289337-chr17:38496323..38498335,2	K562	blood:
4	chr17:38495479..38497798-chr17:38515980..38518835,2	K562	blood:
5	chr17:38455598..38459655-chr17:38495961..38498468,3	K562	blood:

Variant related genes	Relation type
RARA	TF binding region
ENSG00000266208	Chromatin interaction
ENSG00000270145	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11078939	0.80[AMR][1000 genomes]
rs11078940	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12051734	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12103711	0.86[ASN][1000 genomes]
rs12946680	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13706	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16965687	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1807273	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2077464	0.83[ASN][1000 genomes]
rs2120200	0.86[ASN][1000 genomes]
rs28537537	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28663197	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35286757	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36030243	0.86[ASN][1000 genomes]
rs4077125	0.80[AMR][1000 genomes]
rs4566234	0.80[AMR][1000 genomes]
rs55656553	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57179137	0.83[ASN][1000 genomes]
rs58822685	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59490243	0.80[AMR][1000 genomes]
rs60220138	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7217852	0.85[ASN][1000 genomes]
rs72836651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72836653	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72836656	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72836660	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7359537	0.80[EUR][1000 genomes]
rs73983025	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9303285	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9303286	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891694	0.80[AMR][1000 genomes]
rs9892404	0.80[EUR][1000 genomes]
rs9892946	0.80[AMR][1000 genomes]
rs9893520	0.82[EUR][1000 genomes]
rs9894625	0.89[EUR][1000 genomes]
rs9896312	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9897092	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9904270	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9906409	0.82[EUR][1000 genomes]
rs9908257	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9914531	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9916460	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9916782	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1063310	chr17:38467043-38499351	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv1057471	chr17:38467043-38502453	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38485600-38497200	Genic enhancers	Fetal Muscle Leg	muscle
2	chr17:38487200-38497400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr17:38488200-38497000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:38489000-38496800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr17:38489000-38497200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:38489200-38497000	Weak transcription	HSMMtube	muscle
7	chr17:38489600-38497400	Weak transcription	Brain Anterior Caudate	brain
8	chr17:38490200-38497200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:38491000-38497200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr17:38491200-38497200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr17:38491400-38497000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:38491400-38497000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr17:38491400-38497400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:38491600-38496800	Weak transcription	Fetal Kidney	kidney
15	chr17:38491600-38497000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:38491600-38497000	Weak transcription	NH-A	brain
17	chr17:38492000-38497200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr17:38492200-38497000	Weak transcription	Gastric	stomach
19	chr17:38492200-38497000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr17:38492200-38497200	Weak transcription	Aorta	Aorta
21	chr17:38492400-38497000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr17:38492400-38497000	Weak transcription	HUVEC	blood vessel
23	chr17:38492600-38496800	Weak transcription	Hela-S3	cervix
24	chr17:38492800-38497400	Enhancers	Fetal Thymus	thymus
25	chr17:38493000-38496800	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr17:38493000-38497200	Enhancers	Placenta	Placenta
27	chr17:38493200-38497000	Enhancers	Primary hematopoietic stem cells	blood
28	chr17:38493200-38497200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr17:38493200-38497200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr17:38493400-38496800	Genic enhancers	GM12878-XiMat	blood
31	chr17:38493400-38497200	Enhancers	Primary B cells from peripheral blood	blood
32	chr17:38493600-38497200	Enhancers	Psoas Muscle	Psoas
33	chr17:38493800-38497200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:38494000-38497000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:38494000-38497000	Weak transcription	Fetal Brain Male	brain
36	chr17:38494000-38497200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:38494000-38497200	Enhancers	Left Ventricle	heart
38	chr17:38494200-38497200	Weak transcription	Brain Germinal Matrix	brain
39	chr17:38494400-38497200	Weak transcription	Brain Angular Gyrus	brain
40	chr17:38494600-38497000	Weak transcription	Fetal Lung	lung
41	chr17:38494600-38497000	Weak transcription	K562	blood
42	chr17:38494600-38497600	Weak transcription	Dnd41	blood
43	chr17:38494800-38496800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr17:38494800-38496800	Weak transcription	HMEC	breast
45	chr17:38494800-38497000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr17:38494800-38497000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:38494800-38497000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr17:38494800-38497000	Weak transcription	Osteobl	bone
49	chr17:38494800-38497200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:38494800-38497400	Weak transcription	Esophagus	oesophagus

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