Variant report

Variant	rs12509517
Chromosome Location	chr4:103525508-103525509
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103517631..103521191-chr4:103525485..103528516,3	K562	blood:
2	chr4:103420960..103423960-chr4:103524765..103528750,4	MCF-7	breast:
3	chr4:103421575..103424608-chr4:103524149..103526954,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1005819	1.00[JPT][hapmap]
rs1020759	0.90[JPT][hapmap]
rs1020760	1.00[JPT][hapmap]
rs11722146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs118882	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12509403	0.85[CEU][hapmap]
rs12648696	0.94[CHB][hapmap]
rs1585213	0.91[JPT][hapmap]
rs1585215	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1599961	0.91[JPT][hapmap]
rs1609798	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	0.91[JPT][hapmap]
rs170731	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1801	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.86[JPT][hapmap]
rs230491	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs230492	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230495	0.91[JPT][hapmap]
rs230496	0.91[JPT][hapmap]
rs230498	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230500	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230504	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230505	0.91[JPT][hapmap]
rs230509	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230511	0.81[CEU][hapmap]
rs230514	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230515	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs230516	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs230519	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230520	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230521	0.91[JPT][hapmap]
rs230525	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230526	0.91[JPT][hapmap]
rs230528	0.91[JPT][hapmap]
rs230529	0.91[JPT][hapmap]
rs230531	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230532	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230533	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs230534	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs230539	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs230540	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230541	1.00[JPT][hapmap]
rs230542	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774933	0.91[JPT][hapmap]
rs3774936	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3774937	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs3774938	0.91[JPT][hapmap]
rs3774956	1.00[JPT][hapmap]
rs3774959	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774963	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774964	1.00[JPT][hapmap]
rs3817685	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3821958	1.00[JPT][hapmap]
rs4235404	0.80[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	0.91[JPT][hapmap]
rs4648055	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4648058	1.00[JPT][hapmap]
rs4648068	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs4698858	1.00[JPT][hapmap]
rs4698861	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4698863	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4699030	1.00[JPT][hapmap]
rs747559	0.91[JPT][hapmap]
rs9790601	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs980455	0.91[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103483400-103541600	Weak transcription	K562	blood
2	chr4:103497600-103533400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:103500200-103527600	Weak transcription	Pancreas	Pancrea
4	chr4:103500400-103528200	Weak transcription	Right Ventricle	heart
5	chr4:103502600-103532800	Weak transcription	Brain Germinal Matrix	brain
6	chr4:103512600-103527600	Weak transcription	Ovary	ovary
7	chr4:103512800-103531800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:103513000-103542000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:103513200-103536200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:103514400-103526000	Strong transcription	Fetal Intestine Large	intestine
11	chr4:103514600-103535800	Strong transcription	Adipose Nuclei	Adipose
12	chr4:103514600-103538200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:103514600-103539000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:103515000-103539000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:103515200-103533200	Strong transcription	Primary B cells from cord blood	blood
16	chr4:103515200-103533400	Strong transcription	Primary hematopoietic stem cells	blood
17	chr4:103515200-103533600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr4:103515200-103538800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr4:103515400-103533200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:103515400-103533400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:103515400-103533400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:103515400-103533600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:103515400-103538800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:103515400-103538800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:103515600-103533400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:103515600-103535600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr4:103515800-103526600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:103515800-103535800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr4:103515800-103538200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:103515800-103538800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr4:103515800-103538800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr4:103517600-103541600	Weak transcription	Right Atrium	heart
33	chr4:103517800-103536200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:103518000-103528600	Weak transcription	Hela-S3	cervix
35	chr4:103518400-103533200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:103518800-103525600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:103519000-103527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:103519200-103528200	Weak transcription	NHLF	lung
39	chr4:103519400-103527600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:103519600-103528200	Weak transcription	Stomach Mucosa	stomach
41	chr4:103520200-103526400	Weak transcription	Fetal Kidney	kidney
42	chr4:103520200-103527600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:103520200-103528000	Weak transcription	Thymus	Thymus
44	chr4:103520200-103528200	Weak transcription	NH-A	brain
45	chr4:103520200-103530400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:103520200-103535600	Strong transcription	Left Ventricle	heart
47	chr4:103520400-103527400	Weak transcription	Colonic Mucosa	Colon
48	chr4:103520600-103531800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:103520800-103527600	Weak transcription	Fetal Heart	heart
50	chr4:103520800-103527800	Weak transcription	Muscle Satellite Cultured Cells	--

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