Variant report

Variant	rs12646299
Chromosome Location	chr4:88101099-88101100
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	chr4:88099435..88101886-chr4:88139410..88141295,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10001721	0.95[ASN][1000 genomes]
rs10015288	0.95[ASN][1000 genomes]
rs1005808	0.95[ASN][1000 genomes]
rs1037813	1.00[YRI][hapmap]
rs12505327	0.95[ASN][1000 genomes]
rs12505408	0.95[ASN][1000 genomes]
rs12505448	0.92[ASN][1000 genomes]
rs12509389	0.95[ASN][1000 genomes]
rs12509445	0.95[ASN][1000 genomes]
rs12640151	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12645763	0.95[ASN][1000 genomes]
rs12649293	0.85[CEU][hapmap]
rs1552145	0.92[ASN][1000 genomes]
rs1563799	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17604937	1.00[YRI][hapmap]
rs17668731	1.00[YRI][hapmap]
rs17668952	1.00[YRI][hapmap]
rs17703743	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17754784	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17754933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17755005	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]
rs28488787	0.85[ASN][1000 genomes]
rs28495684	0.85[ASN][1000 genomes]
rs28513782	0.95[ASN][1000 genomes]
rs4355355	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4693158	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693804	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4693805	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61734704	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62306545	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62306548	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62308861	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62308864	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62308866	0.96[ASN][1000 genomes]
rs71607411	0.94[ASN][1000 genomes]
rs7698284	0.85[CEU][hapmap]
rs7698923	0.85[CEU][hapmap]
rs967552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:88058200-88109000	Weak transcription	Lung	lung
3	chr4:88061400-88109400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:88063200-88102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:88068000-88116400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:88073400-88113000	Weak transcription	NHDF-Ad	bronchial
7	chr4:88074200-88109400	Weak transcription	Pancreas	Pancrea
8	chr4:88077200-88111000	Weak transcription	Fetal Brain Male	brain
9	chr4:88080600-88101800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:88081800-88140200	Weak transcription	Aorta	Aorta
11	chr4:88082000-88111000	Weak transcription	Brain Germinal Matrix	brain
12	chr4:88082000-88129200	Weak transcription	Esophagus	oesophagus
13	chr4:88082600-88120000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:88082800-88106400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:88083000-88116400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:88084800-88113600	Weak transcription	HSMM	muscle
17	chr4:88085000-88128000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:88086400-88102600	Weak transcription	HSMMtube	muscle
19	chr4:88086600-88109400	Weak transcription	NHLF	lung
20	chr4:88089000-88108400	Weak transcription	Gastric	stomach
21	chr4:88089600-88113600	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:88089600-88131000	Weak transcription	Ovary	ovary
23	chr4:88089800-88106400	Weak transcription	GM12878-XiMat	blood
24	chr4:88089800-88115800	Weak transcription	HepG2	liver
25	chr4:88090000-88107800	Weak transcription	Placenta	Placenta
26	chr4:88090000-88118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:88091200-88111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:88091400-88102000	Weak transcription	Brain Angular Gyrus	brain
29	chr4:88091400-88102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:88091400-88109000	Weak transcription	Fetal Lung	lung
31	chr4:88091400-88118200	Weak transcription	Brain Anterior Caudate	brain
32	chr4:88091800-88104400	Weak transcription	Dnd41	blood
33	chr4:88091800-88106600	Weak transcription	Right Ventricle	heart
34	chr4:88091800-88107600	Weak transcription	Thymus	Thymus
35	chr4:88091800-88115000	Weak transcription	Left Ventricle	heart
36	chr4:88091800-88128000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:88091800-88128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:88091800-88133600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:88092200-88134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:88093000-88113200	Weak transcription	K562	blood
41	chr4:88093800-88113400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:88093800-88119600	Weak transcription	Primary T cells from cord blood	blood
43	chr4:88096800-88115400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr4:88097600-88104000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:88097600-88110200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:88097600-88125200	Weak transcription	Primary B cells from cord blood	blood
47	chr4:88097600-88140400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:88098000-88114800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:88098000-88127400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:88098200-88101200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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