Variant report

Variant	rs1416822
Chromosome Location	chr1:180496295-180496296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180486527..180488396-chr1:180494744..180496710,2	MCF-7	breast:
2	chr1:180495119..180496658-chr1:180599630..180601968,2	K562	blood:
3	chr1:180495342..180496951-chr1:180619499..180622464,2	K562	blood:
4	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction
ENSG00000206905	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10914021	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10914022	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10914035	0.86[EUR][1000 genomes]
rs10914036	0.81[CEU][hapmap]
rs10914038	0.85[EUR][1000 genomes]
rs12027839	0.85[EUR][1000 genomes]
rs12027878	0.85[EUR][1000 genomes]
rs12039331	0.86[CEU][hapmap]
rs12044653	0.85[EUR][1000 genomes]
rs12045365	0.83[EUR][1000 genomes]
rs12407684	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13373944	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13374104	0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13374665	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13376342	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16856127	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17300340	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17300579	1.00[CEU][hapmap]
rs17300600	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17300712	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17372295	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17372362	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17372667	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28816398	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4405110	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4446932	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4651065	0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4652509	0.85[EUR][1000 genomes]
rs56759227	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57537558	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57882351	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58047798	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58089956	0.85[EUR][1000 genomes]
rs58677059	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59022209	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59829460	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60927564	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6425643	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6425646	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6672501	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6680668	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6694454	0.86[EUR][1000 genomes]
rs6697232	0.85[EUR][1000 genomes]
rs6702245	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6704001	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72714834	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72714847	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714855	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714856	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714861	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714864	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714866	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714870	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714877	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714879	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714887	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72714902	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72716607	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72716615	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72716616	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72716625	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716627	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716629	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716632	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72720914	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74132851	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74135185	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7513944	0.81[CEU][hapmap]
rs7517775	1.00[CEU][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7525689	0.94[EUR][1000 genomes]
rs7541993	0.82[CEU][hapmap]
rs7546119	0.81[CEU][hapmap]
rs7547266	0.92[EUR][1000 genomes]
rs7551178	0.82[CEU][hapmap]
rs946631	0.81[CEU][hapmap]
rs946636	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs961162	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9650999	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription 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	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180486000-180499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:180488000-180500400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:180488600-180497000	Enhancers	Placenta	Placenta
4	chr1:180491000-180499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:180491400-180496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
8	chr1:180492400-180496400	Weak transcription	NHEK	skin
9	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
11	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle
12	chr1:180493400-180496600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:180493800-180497000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180494000-180496800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:180494000-180497200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:180494200-180502200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:180494200-180503000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:180494400-180508200	Weak transcription	Right Ventricle	heart
19	chr1:180494600-180497000	Enhancers	Fetal Intestine Small	intestine
20	chr1:180494600-180503000	Weak transcription	Fetal Lung	lung
21	chr1:180494800-180496600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:180494800-180497200	Enhancers	Fetal Intestine Large	intestine
23	chr1:180495000-180497000	Enhancers	Fetal Heart	heart
24	chr1:180495000-180497200	Enhancers	HMEC	breast
25	chr1:180495000-180499200	Weak transcription	Adipose Nuclei	Adipose
26	chr1:180495000-180499200	Weak transcription	Esophagus	oesophagus
27	chr1:180495000-180499200	Weak transcription	Lung	lung
28	chr1:180495000-180502200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:180495000-180503800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:180495200-180502600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:180495400-180496400	Weak transcription	Aorta	Aorta
32	chr1:180495400-180496800	Enhancers	HepG2	liver
33	chr1:180495400-180497000	Enhancers	K562	blood
34	chr1:180495600-180496800	Enhancers	Left Ventricle	heart
35	chr1:180495800-180496600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:180496000-180496600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:180496000-180496600	Enhancers	Right Atrium	heart
38	chr1:180496000-180496800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:180496000-180497000	Enhancers	HSMM	muscle
40	chr1:180496200-180496800	Enhancers	Hela-S3	cervix
41	chr1:180496200-180497000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:180496200-180497000	Enhancers	NH-A	brain
43	chr1:180496200-180497200	Enhancers	A549	lung
44	chr1:180496200-180497200	Enhancers	HUVEC	blood vessel
45	chr1:180496200-180498000	Enhancers	Muscle Satellite Cultured Cells	--

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