Variant report

Variant	rs16961396
Chromosome Location	chr17:17075759-17075760
allele	C/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	CTCF	chr17:17075416-17075771	K562	blood:	n/a	chr17:17075572-17075590 chr17:17075575-17075588

No.	Distal block	Cell Line	Cell type
1	chr17:17071363..17073893-chr17:17074535..17076823,2	K562	blood:
2	chr17:17075295..17076919-chr17:17077058..17080250,3	MCF-7	breast:
3	chr17:17075571..17077759-chr17:17108274..17110785,3	MCF-7	breast:

Variant related genes	Relation type
MPRIP	TF binding region
ENSG00000206859	Chromatin interaction
ENSG00000133030	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12601193	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12601424	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12601453	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602196	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602675	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[MKK][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16961340	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271521	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292527	1.00[ASW][hapmap]
rs2292528	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744124	0.82[CEU][hapmap]
rs3744126	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744135	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744142	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs3803762	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826304	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4078534	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41319048	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316813	0.92[JPT][hapmap]
rs6502557	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7222600	0.82[CEU][hapmap]
rs8064771	0.92[JPT][hapmap]
rs8069241	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8072214	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8076621	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16961396	MIR589	trans	lymphoblastoid	seeQTL
rs16961396	FLCN	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17029800-17088400	Strong transcription	Dnd41	blood
2	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
5	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
7	chr17:17044200-17083600	Strong transcription	Thymus	Thymus
8	chr17:17045000-17088400	Strong transcription	Brain Germinal Matrix	brain
9	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
10	chr17:17051000-17093200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:17053000-17078000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr17:17053200-17088200	Strong transcription	Gastric	stomach
13	chr17:17054800-17087000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:17055200-17089400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr17:17055600-17092600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:17055800-17092600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr17:17056000-17093600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:17056200-17084400	Strong transcription	Aorta	Aorta
19	chr17:17056200-17088200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr17:17056200-17092400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr17:17056400-17078800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr17:17056400-17082400	Strong transcription	Rectal Smooth Muscle	rectum
23	chr17:17056600-17078800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:17056600-17084000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:17056600-17093600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:17056800-17095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:17058200-17075800	Strong transcription	Primary T cells from cord blood	blood
28	chr17:17059400-17089000	Strong transcription	A549	lung
29	chr17:17060400-17088200	Strong transcription	HSMM	muscle
30	chr17:17060400-17093400	Strong transcription	Liver	Liver
31	chr17:17060600-17088800	Strong transcription	Fetal Intestine Small	intestine
32	chr17:17060600-17089200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:17060800-17089000	Strong transcription	NHLF	lung
34	chr17:17060800-17089400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:17060800-17093600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:17061400-17083600	Strong transcription	Esophagus	oesophagus
37	chr17:17061400-17085200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:17061400-17089000	Strong transcription	Osteobl	bone
39	chr17:17061400-17090200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr17:17062800-17085400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:17064800-17083000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr17:17067800-17092200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr17:17069000-17079000	Strong transcription	GM12878-XiMat	blood
44	chr17:17069200-17077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:17070600-17077200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr17:17070600-17078400	Weak transcription	Small Intestine	intestine
47	chr17:17071000-17076000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr17:17071200-17082200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:17071200-17082800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:17071400-17076000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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