Variant report

Variant	rs28438500
Chromosome Location	chr1:155346571-155346572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10158037	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10158433	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13375379	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836851	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16836867	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28491466	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507559	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55641549	0.87[AFR][1000 genomes]
rs56035547	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56770523	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57134822	0.84[AFR][1000 genomes]
rs57519519	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57807227	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58621120	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58647953	0.88[AFR][1000 genomes]
rs58850753	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59633238	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59815288	1.00[AMR][1000 genomes]
rs59913551	0.80[AFR][1000 genomes]
rs59992966	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568057	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60818259	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61403978	0.87[AFR][1000 genomes]
rs61631408	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6427277	0.81[AFR][1000 genomes]
rs6658401	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6659913	0.94[AFR][1000 genomes]
rs6665660	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6665939	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6670530	0.86[AFR][1000 genomes]
rs6692952	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993428	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993486	0.85[AFR][1000 genomes]
rs72995115	0.83[AFR][1000 genomes]
rs72995140	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995165	0.80[AFR][1000 genomes]
rs72995177	0.81[AFR][1000 genomes]
rs73008931	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008968	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73008999	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010906	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010909	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73010921	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7517139	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7517777	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7532714	1.00[AMR][1000 genomes]
rs7541017	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9988453	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers 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	67 gene(s)	inside rSNPs	diseases
3	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	41 gene(s)	inside rSNPs	diseases
5	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	41 gene(s)	inside rSNPs	diseases
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv872467	chr1:155345641-155377171	Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155296200-155349400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:155296600-155348200	Strong transcription	Fetal Stomach	stomach
3	chr1:155297800-155357400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:155299600-155353600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:155303000-155352800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:155306000-155348200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:155306200-155375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:155310000-155347800	Strong transcription	Fetal Intestine Small	intestine
9	chr1:155312400-155407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:155313000-155348400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:155323800-155349400	Strong transcription	Fetal Thymus	thymus
12	chr1:155327800-155347200	Weak transcription	Psoas Muscle	Psoas
13	chr1:155330000-155349000	Weak transcription	Aorta	Aorta
14	chr1:155330200-155362400	Weak transcription	Stomach Mucosa	stomach
15	chr1:155333000-155351200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:155333200-155348800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:155334000-155349600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:155334800-155349600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:155335200-155349200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:155336000-155348200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:155337400-155348200	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:155337600-155347600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:155337600-155350000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:155337800-155348200	Strong transcription	Primary T cells from cord blood	blood
25	chr1:155337800-155348200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:155337800-155348600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:155337800-155350000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:155337800-155351600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:155338000-155348000	Strong transcription	Thymus	Thymus
30	chr1:155338600-155349600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:155339600-155348000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:155339800-155347600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:155340600-155347800	Weak transcription	HMEC	breast
34	chr1:155340600-155361200	Weak transcription	Fetal Heart	heart
35	chr1:155340600-155362600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:155340600-155364200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:155340800-155346800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:155340800-155346800	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:155340800-155349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:155340800-155355600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:155340800-155357600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:155340800-155361800	Weak transcription	Right Ventricle	heart
43	chr1:155340800-155364800	Weak transcription	Small Intestine	intestine
44	chr1:155341200-155347200	Weak transcription	HSMM	muscle
45	chr1:155341600-155349800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:155341600-155351000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:155341800-155348200	Strong transcription	Brain Germinal Matrix	brain
48	chr1:155341800-155349200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:155342000-155348400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:155342000-155350000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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