Variant report

Variant	rs12602196
Chromosome Location	chr17:17045040-17045041
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	chr17:17043821..17046160-chr17:17108071..17109890,2	MCF-7	breast:
2	chr17:17042215..17045044-chr17:17066488..17068871,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf84-2	chr17:17044809-17045074	NONHSAT146048

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12601193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12601424	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12601453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs16961340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16961396	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744124	0.85[CEU][hapmap]
rs3744126	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]
rs3744135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826304	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41319048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316813	1.00[JPT][hapmap]
rs6502557	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6502565	1.00[CEU][hapmap]
rs7222600	1.00[CEU][hapmap]
rs8064771	1.00[JPT][hapmap]
rs8068857	0.84[JPT][hapmap]
rs8069241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8069441	0.84[JPT][hapmap]
rs8072214	0.87[EUR][1000 genomes]
rs8076621	0.87[EUR][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	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	nsv984510	chr17:17015688-17048858	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17024600-17045600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:17029800-17088400	Strong transcription	Dnd41	blood
3	chr17:17030000-17048200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:17030000-17052200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
6	chr17:17030200-17051600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:17030200-17055000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr17:17030400-17047600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:17030400-17047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:17030400-17055800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
12	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
14	chr17:17030600-17051000	Strong transcription	Colonic Mucosa	Colon
15	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr17:17031200-17057200	Strong transcription	Primary T cells from cord blood	blood
17	chr17:17031200-17067800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:17031400-17051800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:17032000-17055000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr17:17032000-17073800	Strong transcription	Fetal Lung	lung
21	chr17:17032200-17048200	Weak transcription	Right Atrium	heart
22	chr17:17032200-17051800	Strong transcription	Pancreas	Pancrea
23	chr17:17032200-17073600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr17:17032400-17051600	Strong transcription	Gastric	stomach
25	chr17:17033400-17051000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr17:17034200-17049400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:17034800-17072800	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr17:17036600-17050200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:17037200-17045600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:17037200-17074200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:17038200-17051600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
33	chr17:17038800-17048400	Weak transcription	Fetal Heart	heart
34	chr17:17038800-17058400	Weak transcription	Fetal Brain Male	brain
35	chr17:17039000-17048200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr17:17039400-17051800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr17:17039800-17047600	Strong transcription	Small Intestine	intestine
38	chr17:17040600-17047400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr17:17041400-17054200	Strong transcription	Hela-S3	cervix
40	chr17:17041600-17045600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr17:17041800-17045800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:17042000-17045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr17:17042200-17045800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:17042200-17046000	Weak transcription	Psoas Muscle	Psoas
45	chr17:17042400-17045200	Genic enhancers	Fetal Thymus	thymus
46	chr17:17042400-17045600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:17042400-17045600	Weak transcription	Ovary	ovary
48	chr17:17042400-17046200	Genic enhancers	HMEC	breast
49	chr17:17042400-17046400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr17:17042400-17046600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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