Variant report

Variant	rs2904423
Chromosome Location	chr16:12351998-12351999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12187862..12189511-chr16:12351608..12352548,6	MCF-7	breast:
2	chr16:12251094..12253122-chr16:12351083..12352799,2	MCF-7	breast:
3	chr16:12188774..12189813-chr16:12351427..12352598,7	MCF-7	breast:
4	chr16:12188978..12189805-chr16:12351807..12352554,2	K562	blood:
5	chr16:12322225..12323263-chr16:12351609..12352580,13	MCF-7	breast:
6	chr16:12322144..12323205-chr16:12351622..12352477,4	MCF-7	breast:
7	chr16:12326297..12328332-chr16:12351704..12354773,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261293	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11075057	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11075058	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11639640	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11644788	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11649626	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11861914	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12148953	0.84[ASN][1000 genomes]
rs12445263	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12445569	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12446650	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12448443	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13335852	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17697005	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17764604	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2089251	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35818743	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4305040	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4780417	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4780418	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781200	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781201	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4781202	0.84[EUR][1000 genomes]
rs6498274	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7189386	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7189945	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7191442	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7192102	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7194718	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7195058	0.82[AMR][1000 genomes]
rs7195520	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7197417	0.83[EUR][1000 genomes]
rs7199556	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7204209	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8061549	0.82[EUR][1000 genomes]
rs8063991	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs869289	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs905950	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9630612	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9921728	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9927705	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9930625	0.82[EUR][1000 genomes]
rs9937220	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12297400-12353800	Weak transcription	Gastric	stomach
2	chr16:12308000-12371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:12309800-12371200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr16:12322600-12353600	Weak transcription	Lung	lung
5	chr16:12323400-12394200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr16:12323800-12373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr16:12330800-12373000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:12333200-12353200	Weak transcription	Spleen	Spleen
9	chr16:12334000-12356600	Weak transcription	Right Atrium	heart
10	chr16:12334400-12356200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:12334600-12371800	Weak transcription	Adipose Nuclei	Adipose
12	chr16:12338200-12356400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
14	chr16:12340400-12353800	Weak transcription	Pancreas	Pancrea
15	chr16:12340800-12353200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:12342400-12352400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr16:12346800-12352000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr16:12346800-12356200	Weak transcription	Fetal Brain Male	brain
19	chr16:12347200-12356200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr16:12347800-12352600	Weak transcription	Brain Germinal Matrix	brain
21	chr16:12347800-12356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
23	chr16:12348200-12371400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr16:12348800-12354200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr16:12349800-12353200	Strong transcription	Primary T cells from cord blood	blood
26	chr16:12349800-12354800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr16:12350000-12354600	Enhancers	Fetal Muscle Leg	muscle
28	chr16:12350200-12354400	Enhancers	Fetal Muscle Trunk	muscle
29	chr16:12350200-12371600	Weak transcription	GM12878-XiMat	blood
30	chr16:12350400-12352600	Enhancers	Placenta	Placenta
31	chr16:12350600-12352200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr16:12350600-12353000	Strong transcription	Primary B cells from cord blood	blood
33	chr16:12350600-12353000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:12350600-12354800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:12350800-12354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr16:12351000-12353800	Enhancers	Brain Angular Gyrus	brain
37	chr16:12351000-12354400	Enhancers	Brain Cingulate Gyrus	brain
38	chr16:12351200-12352600	Enhancers	Fetal Intestine Small	intestine
39	chr16:12351200-12353600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:12351200-12353800	Weak transcription	Esophagus	oesophagus
41	chr16:12351200-12373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:12351200-12382800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:12351400-12356000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr16:12351600-12352000	Enhancers	Fetal Intestine Large	intestine
45	chr16:12351600-12352200	Enhancers	Liver	Liver
46	chr16:12351600-12352200	Enhancers	Fetal Heart	heart
47	chr16:12351600-12352400	Enhancers	Brain Substantia Nigra	brain
48	chr16:12351600-12353200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr16:12351600-12353800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr16:12351800-12352000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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