Variant report

Variant	rs830717
Chromosome Location	chr16:12323309-12323310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12322209..12324373-chr16:12327262..12329286,2	MCF-7	breast:
2	chr16:12188832..12189545-chr16:12322442..12323344,2	MCF-7	breast:
3	chr16:12322281..12324102-chr16:12364596..12366480,2	MCF-7	breast:
4	chr16:12321706..12323934-chr16:12329346..12331176,2	MCF-7	breast:
5	chr16:12189228..12190118-chr16:12322836..12323693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261293	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1701134	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1704137	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2941081	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2941082	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2941085	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830715	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830718	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830719	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs830720	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830727	0.90[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs830735	0.84[EUR][1000 genomes]
rs864935	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][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	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv905348	chr16:12299936-12358206	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12297400-12353800	Weak transcription	Gastric	stomach
2	chr16:12306200-12323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:12306400-12330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:12308000-12371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:12309800-12371200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr16:12310600-12328600	Weak transcription	Aorta	Aorta
7	chr16:12311800-12333400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr16:12313800-12329800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr16:12314000-12329000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr16:12319400-12327800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr16:12319600-12327600	Weak transcription	GM12878-XiMat	blood
12	chr16:12319800-12323800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr16:12319800-12324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr16:12319800-12328600	Weak transcription	Brain Angular Gyrus	brain
15	chr16:12320000-12323600	Weak transcription	Brain Substantia Nigra	brain
16	chr16:12320200-12323600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr16:12320200-12332600	Weak transcription	Brain Germinal Matrix	brain
18	chr16:12320400-12323600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr16:12320600-12325000	Weak transcription	Osteobl	bone
20	chr16:12320800-12324600	Enhancers	Placenta	Placenta
21	chr16:12321200-12325200	Weak transcription	HSMMtube	muscle
22	chr16:12321800-12323600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr16:12321800-12324000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr16:12321800-12324600	Enhancers	Fetal Intestine Large	intestine
25	chr16:12321800-12324600	Enhancers	Fetal Intestine Small	intestine
26	chr16:12321800-12325200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr16:12321800-12327000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr16:12322000-12323400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr16:12322000-12323800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr16:12322000-12324400	Enhancers	Duodenum Mucosa	Duodenum
31	chr16:12322000-12325000	Enhancers	Fetal Stomach	stomach
32	chr16:12322000-12325400	Weak transcription	HSMM	muscle
33	chr16:12322000-12326400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:12322000-12326600	Enhancers	NHDF-Ad	bronchial
35	chr16:12322200-12323400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr16:12322200-12323400	Enhancers	Brain Hippocampus Middle	brain
37	chr16:12322200-12323600	Enhancers	Stomach Smooth Muscle	stomach
38	chr16:12322200-12323800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr16:12322200-12323800	Enhancers	Thymus	Thymus
40	chr16:12322200-12324200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr16:12322200-12324200	Enhancers	A549	lung
42	chr16:12322200-12324400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr16:12322200-12326800	Enhancers	NHLF	lung
44	chr16:12322400-12323600	Weak transcription	Fetal Kidney	kidney
45	chr16:12322400-12323800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr16:12322400-12323800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr16:12322400-12323800	Enhancers	Colonic Mucosa	Colon
48	chr16:12322400-12323800	Flanking Active TSS	HepG2	liver
49	chr16:12322400-12324600	Enhancers	Ovary	ovary
50	chr16:12322400-12325800	Strong transcription	Primary B cells from peripheral blood	blood

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