Variant report

Variant	rs9896312
Chromosome Location	chr17:38486001-38486002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38335516..38337766-chr17:38485311..38488142,2	MCF-7	breast:
2	chr17:38135905..38138929-chr17:38484621..38486830,3	K562	blood:

Variant related genes	Relation type
ENSG00000108352	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11078940	0.84[AMR][1000 genomes]
rs12051734	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12103711	0.90[ASN][1000 genomes]
rs12946680	0.91[ASN][1000 genomes]
rs13706	0.88[ASN][1000 genomes]
rs1807273	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2077464	0.86[ASN][1000 genomes]
rs2120200	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35286757	0.95[ASN][1000 genomes]
rs36030243	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4134994	0.83[ASN][1000 genomes]
rs55656553	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57179137	0.86[ASN][1000 genomes]
rs58822685	0.83[AMR][1000 genomes]
rs59406133	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60220138	0.87[AMR][1000 genomes]
rs7217852	0.88[ASN][1000 genomes]
rs72836651	0.87[AMR][1000 genomes]
rs72836653	0.84[AMR][1000 genomes]
rs72836656	0.83[AMR][1000 genomes]
rs72836660	0.87[AMR][1000 genomes]
rs73983025	0.83[AMR][1000 genomes]
rs9303285	0.83[ASN][1000 genomes]
rs9303286	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9894625	0.81[ASN][1000 genomes]
rs9904270	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9908257	0.87[AMR][1000 genomes]
rs9914531	0.83[AMR][1000 genomes]
rs9916460	0.83[AMR][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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38474800-38487000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr17:38479200-38494400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:38479400-38486600	Weak transcription	Fetal Brain Male	brain
4	chr17:38479400-38489600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr17:38479400-38491600	Enhancers	Fetal Heart	heart
6	chr17:38479600-38487600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:38479600-38490200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr17:38479600-38491200	Weak transcription	Fetal Kidney	kidney
9	chr17:38479800-38488200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:38480000-38486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr17:38480000-38487000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:38480000-38487200	Enhancers	Fetal Thymus	thymus
13	chr17:38480000-38487600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:38480400-38486200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:38480400-38487200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:38480400-38487400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:38480800-38487400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:38481000-38486200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr17:38481600-38487200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr17:38482600-38486200	Weak transcription	Brain Angular Gyrus	brain
21	chr17:38482800-38486200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr17:38483000-38486200	Enhancers	Primary B cells from peripheral blood	blood
23	chr17:38483200-38486200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr17:38483200-38486200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:38483200-38486200	Weak transcription	Dnd41	blood
26	chr17:38483200-38486200	Weak transcription	HMEC	breast
27	chr17:38483200-38486200	Weak transcription	HUVEC	blood vessel
28	chr17:38483200-38487400	Weak transcription	Aorta	Aorta
29	chr17:38483400-38486200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:38483400-38486200	Weak transcription	Hela-S3	cervix
31	chr17:38483400-38486600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr17:38483400-38490800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:38483600-38486200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr17:38483600-38486200	Weak transcription	NH-A	brain
35	chr17:38483800-38486200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr17:38484000-38486200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr17:38484000-38486200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr17:38484000-38486200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr17:38484000-38486200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:38484000-38486200	Enhancers	A549	lung
41	chr17:38484000-38486400	Enhancers	Liver	Liver
42	chr17:38484000-38486400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr17:38484000-38491600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:38484200-38486200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:38484200-38486200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:38484200-38486200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:38484200-38486200	Weak transcription	Fetal Intestine Large	intestine
48	chr17:38484200-38486200	Weak transcription	Fetal Intestine Small	intestine
49	chr17:38484200-38486200	Weak transcription	K562	blood
50	chr17:38484200-38486400	Enhancers	Primary T helper cells PMA-I stimulated	--

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