Variant report

Variant	rs28427870
Chromosome Location	chr1:153508400-153508401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:67)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:67 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr1:153508179..153508865-chr16:18812373..18813326,2	Hela-S3	cervix:
2	chr1:153508236..153509740-chr1:153522237..153524623,2	K562	blood:
3	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
4	chr1:153507285..153510261-chr1:153579792..153582160,3	MCF-7	breast:
5	chr1:153507494..153508418-chr11:126173674..126174307,2	Hela-S3	cervix:
6	chr1:153507658..153508549-chr15:72977999..72978681,2	Hela-S3	cervix:
7	chr1:151227011..151227565-chr1:153507831..153508764,2	Hela-S3	cervix:
8	chr1:153508168..153508824-chr6:106773337..106774109,2	Hela-S3	cervix:
9	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
10	chr1:153507994..153509209-chr19:17622174..17622791,3	Hela-S3	cervix:
11	chr1:153507948..153508566-chr8:120844632..120845145,2	Hela-S3	cervix:
12	chr1:153507926..153508844-chr7:6523134..6524128,2	Hela-S3	cervix:
13	chr1:153507935..153508859-chr6:86387943..86388842,2	Hela-S3	cervix:
14	chr1:64058939..64059975-chr1:153508278..153509068,3	Hela-S3	cervix:
15	chr1:153507595..153508673-chr1:153589169..153590111,3	Hela-S3	cervix:
16	chr1:153508087..153508640-chr11:68227915..68228540,2	Hela-S3	cervix:
17	chr1:153508057..153508831-chr5:34914838..34915676,2	Hela-S3	cervix:
18	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
19	chr1:153508098..153508656-chr2:48667782..48668296,2	Hela-S3	cervix:
20	chr1:153507987..153508581-chr2:128051374..128052175,2	HCT-116	colon:
21	chr1:153507839..153508678-chr5:1523284..1524135,2	Hela-S3	cervix:
22	chr1:153507740..153508606-chr9:140135003..140135854,2	Hela-S3	cervix:
23	chr1:26185351..26185971-chr1:153508112..153508749,2	HCT-116	colon:
24	chr1:153508165..153508666-chr6:24667045..24667545,2	Hela-S3	cervix:
25	chr1:153507935..153508866-chr6:17705709..17706691,3	Hela-S3	cervix:
26	chr1:153507728..153508719-chr17:48944286..48945252,3	Hela-S3	cervix:
27	chr1:153508082..153508658-chr11:66383693..66384529,2	Hela-S3	cervix:
28	chr1:153507944..153508640-chr10:43903183..43903757,2	Hela-S3	cervix:
29	chr1:153507569..153508511-chr17:41465308..41465853,2	Hela-S3	cervix:
30	chr1:153507953..153508555-chr6:74230351..74231122,2	Hela-S3	cervix:
31	chr1:153507821..153508588-chr1:236444774..236445391,2	Hela-S3	cervix:
32	chr1:153508215..153509143-chr4:100870830..100871549,2	Hela-S3	cervix:
33	chr1:153508043..153508984-chr15:83478155..83479111,2	Hela-S3	cervix:
34	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
35	chr1:153508212..153508984-chr1:201979397..201980003,2	Hela-S3	cervix:
36	chr1:153507982..153508601-chr19:47616487..47617087,2	Hela-S3	cervix:
37	chr1:153508300..153508852-chr17:80186804..80187510,2	Hela-S3	cervix:
38	chr1:153508015..153508858-chr11:65728937..65729487,2	Hela-S3	cervix:
39	chr1:153508046..153508700-chr16:30907732..30908480,2	Hela-S3	cervix:
40	chr1:153508232..153508742-chr21:17102120..17102741,2	Hela-S3	cervix:
41	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
42	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
43	chr1:153508398..153508913-chr2:240323217..240323772,2	Hela-S3	cervix:
44	chr1:91486844..91487514-chr1:153508094..153508697,2	HCT-116	colon:
45	chr1:153508083..153508629-chr3:49449020..49449991,2	Hela-S3	cervix:
46	chr1:153508026..153508716-chr6:26123404..26124166,2	Hela-S3	cervix:
47	chr1:153507840..153508475-chr1:153581398..153581986,2	Hela-S3	cervix:
48	chr1:153507997..153508727-chr12:6643447..6644057,2	Hela-S3	cervix:
49	chr1:153508391..153508964-chr17:62223072..62223763,2	Hela-S3	cervix:
50	chr1:153507893..153508609-chr16:31518849..31519689,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000079739	Chromatin interaction
ENSG00000189143	Chromatin interaction
ENSG00000142230	Chromatin interaction
ENSG00000057663	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000140941	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000130313	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000064313	Chromatin interaction
ENSG00000145779	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000272269	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000169813	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000150281	Chromatin interaction
ENSG00000110075	Chromatin interaction
ENSG00000113460	Chromatin interaction
ENSG00000234678	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000124789	Chromatin interaction
ENSG00000141526	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000068024	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000209042	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000113456	Chromatin interaction
ENSG00000111640	Chromatin interaction
ENSG00000255062	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000221886	Chromatin interaction
ENSG00000142856	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000269439	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000112029	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000130749	Chromatin interaction
ENSG00000227627	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000086619	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000127423	Chromatin interaction
ENSG00000155313	Chromatin interaction
ENSG00000163435	Chromatin interaction
ENSG00000175202	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000122482	Chromatin interaction
ENSG00000177410	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000222020	Chromatin interaction
ENSG00000136240	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2248745	0.93[ASN][1000 genomes]
rs2480695	0.93[ASN][1000 genomes]
rs2480696	0.93[ASN][1000 genomes]
rs28483109	0.93[ASN][1000 genomes]
rs3762262	0.93[ASN][1000 genomes]
rs4017737	0.93[ASN][1000 genomes]
rs477339	0.93[ASN][1000 genomes]
rs550597	0.83[ASN][1000 genomes]
rs552446	0.93[ASN][1000 genomes]
rs585215	0.93[ASN][1000 genomes]
rs659403	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:158 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153505400-153508400	Flanking Active TSS	NH-A	brain
2	chr1:153505600-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:153505800-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:153505800-153508400	Flanking Active TSS	Osteobl	bone
5	chr1:153505800-153509200	Active TSS	Aorta	Aorta
6	chr1:153505800-153509400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr1:153506000-153508400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
8	chr1:153506200-153508400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
9	chr1:153506800-153508400	Transcr. at gene 5' and 3'	NHEK	skin
10	chr1:153506800-153509000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:153506800-153509200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:153507000-153509200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:153507000-153509400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:153507200-153509000	Flanking Active TSS	Spleen	Spleen
15	chr1:153507200-153509200	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr1:153507400-153508400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr1:153507400-153508400	Flanking Active TSS	Right Ventricle	heart
18	chr1:153507400-153509400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:153507400-153509600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:153507600-153508400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:153507600-153508400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:153507600-153508400	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr1:153507600-153508400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:153507600-153508400	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr1:153507600-153508400	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr1:153507600-153508400	Flanking Active TSS	Fetal Intestine Large	intestine
27	chr1:153507600-153508400	Flanking Active TSS	Fetal Lung	lung
28	chr1:153507600-153508400	Flanking Active TSS	Placenta	Placenta
29	chr1:153507600-153508400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
30	chr1:153507600-153508600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:153507600-153508800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:153507600-153508800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:153507600-153508800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr1:153507600-153508800	Active TSS	A549	lung
35	chr1:153507600-153509000	Active TSS	Fetal Kidney	kidney
36	chr1:153507600-153509000	Active TSS	Placenta Amnion	Placenta Amnion
37	chr1:153507600-153509000	Active TSS	Small Intestine	intestine
38	chr1:153507600-153509200	Flanking Active TSS	Fetal Thymus	thymus
39	chr1:153507600-153509400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr1:153507600-153509400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:153507600-153509400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:153507600-153509400	Flanking Active TSS	Esophagus	oesophagus
43	chr1:153507800-153508400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:153507800-153508400	Flanking Active TSS	Right Atrium	heart
45	chr1:153507800-153508400	Flanking Active TSS	GM12878-XiMat	blood
46	chr1:153507800-153508600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:153507800-153508600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:153507800-153508800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:153507800-153508800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr1:153507800-153508800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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