Variant report

Variant	rs3744126
Chromosome Location	chr17:17093309-17093310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17090881..17093719-chr17:17108293..17110165,2	K562	blood:
2	chr17:17084528..17086994-chr17:17091747..17094642,2	K562	blood:
3	chr17:17092917..17095538-chr17:17100650..17103433,2	MCF-7	breast:
4	chr17:17088597..17090779-chr17:17091806..17094698,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf84-1	chr17:17091982-17095962	ENSG00000259850.1

Variant related genes	Relation type
ENSG00000263624	Chromatin interaction
ENSG00000133030	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12601193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12601424	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12601453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs16961340	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16961396	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271521	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744124	0.85[CEU][hapmap]
rs3744135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744142	0.86[CHB][hapmap]
rs3803762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41319048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4316813	0.92[JPT][hapmap]
rs6502557	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs6502565	1.00[CEU][hapmap]
rs7222600	1.00[CEU][hapmap]
rs8064771	0.92[JPT][hapmap]
rs8069241	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8072214	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8076621	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
2	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
3	chr17:17056000-17093600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:17056600-17093600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:17056800-17095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:17060400-17093400	Strong transcription	Liver	Liver
7	chr17:17060800-17093600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:17076200-17094600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:17076600-17104600	Weak transcription	K562	blood
10	chr17:17084400-17093400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:17084400-17095200	Weak transcription	Fetal Kidney	kidney
12	chr17:17084800-17094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:17084800-17094800	Weak transcription	Fetal Brain Male	brain
14	chr17:17085600-17094800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:17086400-17095200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:17086400-17104800	Weak transcription	Brain Substantia Nigra	brain
17	chr17:17086400-17106600	Weak transcription	Colonic Mucosa	Colon
18	chr17:17086600-17094800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:17087200-17094800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:17087600-17093800	Enhancers	Fetal Heart	heart
21	chr17:17087600-17093800	Genic enhancers	HSMMtube	muscle
22	chr17:17087600-17095400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:17087800-17093800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:17087800-17094800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr17:17088000-17093600	Weak transcription	NHDF-Ad	bronchial
26	chr17:17088000-17093800	Genic enhancers	Placenta	Placenta
27	chr17:17088000-17094000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr17:17088200-17093400	Weak transcription	Psoas Muscle	Psoas
29	chr17:17088200-17093800	Weak transcription	Brain Anterior Caudate	brain
30	chr17:17088400-17093600	Strong transcription	Thymus	Thymus
31	chr17:17088800-17093400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr17:17089200-17093800	Genic enhancers	HMEC	breast
33	chr17:17089400-17093600	Strong transcription	Dnd41	blood
34	chr17:17089400-17093800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:17089400-17093800	Genic enhancers	HSMM	muscle
36	chr17:17089400-17094000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr17:17089400-17095200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:17089600-17094800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr17:17089600-17096600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr17:17089800-17093800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr17:17089800-17094000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr17:17089800-17094400	Strong transcription	Primary T cells from cord blood	blood
43	chr17:17090000-17093800	Strong transcription	Fetal Intestine Small	intestine
44	chr17:17090000-17094000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr17:17090200-17094000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:17090200-17107000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr17:17090200-17107400	Weak transcription	Small Intestine	intestine
48	chr17:17090400-17093800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr17:17090600-17093400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:17090600-17095600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links