Variant report

Variant	rs28816398
Chromosome Location	chr1:180430592-180430593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10914021	0.84[EUR][1000 genomes]
rs10914022	0.83[EUR][1000 genomes]
rs13373944	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13374104	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13374665	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13376342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1416822	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17300282	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17300340	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17300600	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17300712	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17372281	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17372295	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17372362	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17372667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4405110	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4446932	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4651065	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56759227	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57537558	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57882351	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58047798	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58677059	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59022209	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59113753	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59829460	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60927564	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6425643	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6672501	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6674374	0.83[AFR][1000 genomes]
rs6680668	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6694896	0.90[EUR][1000 genomes]
rs6702245	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6704001	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72712995	0.88[EUR][1000 genomes]
rs72713000	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72714804	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72714834	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72714847	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714855	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714856	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714861	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714864	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714866	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714870	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714877	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714879	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714887	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72714902	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72716615	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72716616	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72716625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72716627	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72716629	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72716632	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72720914	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74132851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74135185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7517775	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7525689	0.84[EUR][1000 genomes]
rs7547266	0.81[EUR][1000 genomes]
rs946636	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs961162	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9650999	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:180392600-180446200	Weak transcription	K562	blood
3	chr1:180403400-180431200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180403400-180448000	Weak transcription	HMEC	breast
5	chr1:180404200-180431800	Weak transcription	NHEK	skin
6	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
7	chr1:180417600-180431200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:180418000-180431200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:180418400-180430800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:180421000-180430600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:180421000-180431200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:180421000-180431800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:180421000-180448000	Weak transcription	HSMM	muscle
14	chr1:180421200-180431200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:180421200-180431200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:180421200-180431400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:180421200-180431800	Weak transcription	A549	lung
18	chr1:180421200-180451600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:180421400-180431000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:180421600-180430600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:180421600-180431200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:180421600-180431200	Weak transcription	Ovary	ovary
23	chr1:180422200-180430600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:180423000-180430600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:180424400-180430800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:180425600-180431400	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:180425800-180457600	Weak transcription	Aorta	Aorta
28	chr1:180426600-180430600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:180426600-180430600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:180426600-180431000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:180426600-180431000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:180426600-180431600	Weak transcription	Dnd41	blood
33	chr1:180426800-180431400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:180427400-180448200	Weak transcription	Osteobl	bone
35	chr1:180428000-180470000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:180428600-180438000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:180429400-180430600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:180429400-180430600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:180429400-180430600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:180429400-180431400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
41	chr1:180429400-180435200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:180429600-180431000	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr1:180429600-180431200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:180429600-180431400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr1:180429600-180444600	Weak transcription	Esophagus	oesophagus
46	chr1:180429600-180455000	Weak transcription	Left Ventricle	heart
47	chr1:180429800-180431000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:180429800-180431600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr1:180430200-180430800	Weak transcription	Lung	lung
50	chr1:180430200-180431800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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