Variant report

Variant	rs510209
Chromosome Location	chr1:179935415-179935416
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	chr1:179922758..179925487-chr1:179931263..179936967,5	MCF-7	breast:
2	chr1:179927273..179932264-chr1:179932290..179936939,6	K562	blood:

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10753206	0.80[CEU][hapmap]
rs10798729	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10798732	0.89[CEU][hapmap]
rs10913916	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10913917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913918	0.94[JPT][hapmap]
rs10913927	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12040314	0.88[CEU][hapmap]
rs12040376	0.88[CEU][hapmap]
rs12075450	0.81[JPT][hapmap]
rs1281384	0.81[JPT][hapmap]
rs1281389	0.81[JPT][hapmap]
rs1292777	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1297205	0.88[CEU][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1631932	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981314	0.81[JPT][hapmap]
rs2281805	0.81[JPT][hapmap]
rs2319676	0.85[JPT][hapmap]
rs2477106	0.94[JPT][hapmap]
rs2477110	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2477111	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477112	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477116	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2477117	0.81[JPT][hapmap]
rs2477118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477119	0.93[JPT][hapmap]
rs2477120	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483621	0.95[EUR][1000 genomes]
rs2483622	0.94[JPT][hapmap]
rs2501607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2501608	0.94[JPT][hapmap]
rs2501610	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2501611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2501613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2501615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501616	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2501617	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2501620	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501621	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2762859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767200	0.80[EUR][1000 genomes]
rs3767201	0.81[JPT][hapmap]
rs3767202	0.81[EUR][1000 genomes]
rs3818999	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3930305	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4076449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147169	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4256775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4263962	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs4336810	0.88[CEU][hapmap]
rs4379644	0.81[JPT][hapmap]
rs4506429	0.89[CEU][hapmap]
rs4651054	0.85[EUR][1000 genomes]
rs4651055	0.81[JPT][hapmap]
rs4652457	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652462	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4652463	0.82[EUR][1000 genomes]
rs4652465	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4652471	0.89[CEU][hapmap]
rs483307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498625	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500371	0.84[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs504202	0.81[JPT][hapmap]
rs521858	0.81[JPT][hapmap]
rs526683	0.86[JPT][hapmap]
rs528350	0.92[CEU][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs533795	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs534168	0.89[CEU][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs551607	0.81[JPT][hapmap]
rs552743	0.81[JPT][hapmap]
rs561233	0.81[JPT][hapmap]
rs6425603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6425609	0.96[CEU][hapmap]
rs6657347	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs6660984	0.87[JPT][hapmap]
rs6676989	0.80[JPT][hapmap]
rs6691435	0.88[CEU][hapmap]
rs6692394	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7521895	0.81[JPT][hapmap]
rs7521948	0.81[JPT][hapmap]
rs7524849	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7551181	0.92[CEU][hapmap]
rs9286932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9425481	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9425482	0.81[EUR][1000 genomes]
rs9425485	0.88[CEU][hapmap]
rs9425849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425851	0.84[EUR][1000 genomes]
rs9425853	0.81[JPT][hapmap]
rs9425854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9425855	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425856	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425861	0.96[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs9425868	0.88[CEU][hapmap]

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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:179924800-179937800	Weak transcription	Spleen	Spleen
3	chr1:179924800-179938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:179924800-179938000	Weak transcription	Lung	lung
5	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
7	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:179925600-179935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:179925600-179938400	Weak transcription	HSMM	muscle
10	chr1:179925800-179935600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:179925800-179935600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:179925800-179937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:179925800-179937600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:179925800-179937600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:179925800-179937800	Weak transcription	Thymus	Thymus
16	chr1:179925800-179940600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:179926000-179937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:179926000-179938000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:179926000-179938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:179926000-179938000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:179926000-179938000	Weak transcription	Right Atrium	heart
22	chr1:179926000-179938200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:179926000-179938400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:179926400-179937800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:179926800-179961400	Weak transcription	A549	lung
26	chr1:179927000-179935600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:179927000-179935600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:179927000-179935600	Weak transcription	K562	blood
29	chr1:179927000-179937800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:179927000-179965600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:179927200-179937600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:179927200-179940600	Weak transcription	NHDF-Ad	bronchial
33	chr1:179928000-179935800	Weak transcription	Fetal Lung	lung
34	chr1:179928000-179939000	Weak transcription	Fetal Heart	heart
35	chr1:179928600-179937200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:179928600-179937200	Weak transcription	Left Ventricle	heart
37	chr1:179928600-179937800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:179928800-179937800	Weak transcription	Psoas Muscle	Psoas
39	chr1:179929600-179935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:179931200-179935600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:179931200-179935600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:179931400-179935600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:179931400-179935600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:179931400-179935600	Weak transcription	Fetal Intestine Large	intestine
45	chr1:179931400-179936600	Weak transcription	Fetal Stomach	stomach
46	chr1:179931600-179938000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:179931800-179937600	Weak transcription	Ovary	ovary
48	chr1:179933600-179935800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:179933800-179937800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:179934000-179937800	Weak transcription	Brain Cingulate Gyrus	brain

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