Variant report

Variant	rs12028408
Chromosome Location	chr1:185149263-185149264
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	chr1:185147958..185150868-chr1:185161570..185163115,2	K562	blood:
2	chr1:185013445..185015257-chr1:185149259..185152347,3	K562	blood:

Variant related genes	Relation type
ENSG00000121481	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10218496	0.84[EUR][1000 genomes]
rs10453829	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10489579	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10489580	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024023	0.93[EUR][1000 genomes]
rs12045671	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12096987	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12118722	0.82[EUR][1000 genomes]
rs12119471	0.82[EUR][1000 genomes]
rs12127840	0.82[EUR][1000 genomes]
rs12135172	0.82[EUR][1000 genomes]
rs12141722	0.96[EUR][1000 genomes]
rs12404187	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415072	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1591585	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1969750	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2025227	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050566	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2146328	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2383269	0.84[EUR][1000 genomes]
rs3766717	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57188163	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57731138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6424972	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6424974	0.82[EUR][1000 genomes]
rs6660169	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6666742	0.82[EUR][1000 genomes]
rs6670117	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6673303	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698109	0.98[EUR][1000 genomes]
rs6698122	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7512290	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522617	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7533198	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539658	0.82[EUR][1000 genomes]
rs7543962	0.98[EUR][1000 genomes]
rs7550586	0.82[EUR][1000 genomes]
rs7550599	0.80[EUR][1000 genomes]
rs7552662	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7556183	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs951428	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127200-185169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:185127400-185152200	Weak transcription	Aorta	Aorta
3	chr1:185127400-185153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:185127400-185157400	Weak transcription	Small Intestine	intestine
5	chr1:185127400-185163400	Weak transcription	Esophagus	oesophagus
6	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:185127600-185170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
9	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
10	chr1:185128000-185166400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:185128200-185153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:185128200-185161200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:185128400-185155200	Weak transcription	NHDF-Ad	bronchial
14	chr1:185128400-185193800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:185128400-185201800	Weak transcription	Gastric	stomach
16	chr1:185128600-185168200	Weak transcription	Fetal Heart	heart
17	chr1:185128600-185171400	Weak transcription	Fetal Brain Male	brain
18	chr1:185131600-185173000	Weak transcription	Brain Substantia Nigra	brain
19	chr1:185132000-185155800	Weak transcription	HSMMtube	muscle
20	chr1:185134000-185170600	Weak transcription	Lung	lung
21	chr1:185134600-185193200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:185134800-185159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:185135000-185162800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:185136600-185167200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:185136800-185171200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:185137200-185166800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:185137200-185177200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:185137200-185191400	Weak transcription	Brain Anterior Caudate	brain
29	chr1:185137400-185152200	Weak transcription	Ovary	ovary
30	chr1:185137400-185154600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:185137400-185160000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:185137400-185160200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:185137400-185168000	Weak transcription	Fetal Intestine Large	intestine
34	chr1:185137400-185177400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:185137400-185191200	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:185137400-185191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:185138000-185153000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:185138000-185157400	Weak transcription	HUVEC	blood vessel
39	chr1:185138000-185182200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:185138000-185186200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:185138000-185204000	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:185138200-185171400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:185138800-185154000	Weak transcription	Liver	Liver
44	chr1:185139600-185159200	Weak transcription	Fetal Brain Female	brain
45	chr1:185139600-185177400	Weak transcription	Fetal Kidney	kidney
46	chr1:185139800-185151000	Weak transcription	Left Ventricle	heart
47	chr1:185139800-185152600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:185139800-185156200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:185139800-185165400	Weak transcription	Thymus	Thymus
50	chr1:185139800-185167000	Weak transcription	Fetal Lung	lung

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