Variant report

Variant	rs659403
Chromosome Location	chr1:153507959-153507960
allele	C/G
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:43)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:43 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
2	chr1:153507285..153510261-chr1:153579792..153582160,3	MCF-7	breast:
3	chr1:153507494..153508418-chr11:126173674..126174307,2	Hela-S3	cervix:
4	chr1:153507658..153508549-chr15:72977999..72978681,2	Hela-S3	cervix:
5	chr1:151227011..151227565-chr1:153507831..153508764,2	Hela-S3	cervix:
6	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
7	chr1:153505870..153508233-chr1:153598440..153600666,2	MCF-7	breast:
8	chr1:153507948..153508566-chr8:120844632..120845145,2	Hela-S3	cervix:
9	chr1:153507926..153508844-chr7:6523134..6524128,2	Hela-S3	cervix:
10	chr1:153507935..153508859-chr6:86387943..86388842,2	Hela-S3	cervix:
11	chr1:153507595..153508673-chr1:153589169..153590111,3	Hela-S3	cervix:
12	chr1:153507839..153508364-chr6:31632486..31633062,2	Hela-S3	cervix:
13	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
14	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
15	chr1:153507839..153508678-chr5:1523284..1524135,2	Hela-S3	cervix:
16	chr1:153507740..153508606-chr9:140135003..140135854,2	Hela-S3	cervix:
17	chr1:153507935..153508866-chr6:17705709..17706691,3	Hela-S3	cervix:
18	chr1:153507728..153508719-chr17:48944286..48945252,3	Hela-S3	cervix:
19	chr1:153507944..153508640-chr10:43903183..43903757,2	Hela-S3	cervix:
20	chr1:153507569..153508511-chr17:41465308..41465853,2	Hela-S3	cervix:
21	chr1:153507953..153508555-chr6:74230351..74231122,2	Hela-S3	cervix:
22	chr1:153507821..153508588-chr1:236444774..236445391,2	Hela-S3	cervix:
23	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
24	chr1:153507319..153508218-chr15:65596903..65597603,2	Hela-S3	cervix:
25	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
26	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
27	chr1:153507293..153508252-chr10:43932246..43932760,2	Hela-S3	cervix:
28	chr1:153506299..153508188-chr1:153578857..153582741,3	K562	blood:
29	chr1:153507840..153508475-chr1:153581398..153581986,2	Hela-S3	cervix:
30	chr1:153507471..153508095-chr5:133860277..133861255,2	Hela-S3	cervix:
31	chr1:153507893..153508609-chr16:31518849..31519689,2	Hela-S3	cervix:
32	chr1:153507573..153508516-chr19:39897129..39898056,2	Hela-S3	cervix:
33	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
34	chr1:153507643..153508242-chr6:27107630..27108148,2	Hela-S3	cervix:
35	chr1:153507230..153509062-chr1:153605925..153607769,2	MCF-7	breast:
36	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
37	chr1:153507779..153508454-chr12:52541861..52542445,2	Hela-S3	cervix:
38	chr1:153507404..153508006-chr5:41869991..41870750,2	Hela-S3	cervix:
39	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:
40	chr1:153507922..153508745-chr6:27106854..27107517,2	Hela-S3	cervix:
41	chr1:153507784..153508663-chr6:28864170..28864812,2	Hela-S3	cervix:
42	chr1:153507550..153508606-chr1:153517687..153518604,3	Hela-S3	cervix:
43	chr1:45196436..45197066-chr1:153507531..153508059,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000188229	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000272269	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000064313	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000175202	Chromatin interaction
ENSG00000086619	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000255062	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000169813	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000243660	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000124789	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000248668	Chromatin interaction
ENSG00000136240	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs16835393	0.91[CEU][hapmap]
rs17695220	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs1810765	1.00[JPT][hapmap]
rs1887039	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs2094217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248745	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262587	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339696	0.86[AMR][1000 genomes]
rs2480695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480696	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28464843	0.88[AMR][1000 genomes]
rs28483109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4430277	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs477339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845351	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs4845352	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs4845554	0.86[CEU][hapmap]
rs4845555	0.80[AMR][1000 genomes]
rs532652	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587743	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs6659755	0.86[AMR][1000 genomes]
rs6684970	0.91[CEU][hapmap]
rs6690638	0.80[AMR][1000 genomes]
rs6690712	0.80[AMR][1000 genomes]
rs7515940	0.81[AMR][1000 genomes]
rs7518306	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs7520093	0.88[AMR][1000 genomes]
rs7534343	0.88[AMR][1000 genomes]
rs7534347	0.88[AMR][1000 genomes]
rs7537898	0.81[AMR][1000 genomes]
rs7544359	0.81[AMR][1000 genomes]
rs9426945	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153504800-153508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:153505400-153508000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr1:153505400-153508000	Enhancers	Fetal Heart	heart
4	chr1:153505400-153508200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:153505400-153508200	Flanking Active TSS	Colonic Mucosa	Colon
6	chr1:153505400-153508400	Flanking Active TSS	NH-A	brain
7	chr1:153505600-153508000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:153505600-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:153505800-153508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:153505800-153508400	Flanking Active TSS	Osteobl	bone
11	chr1:153505800-153509200	Active TSS	Aorta	Aorta
12	chr1:153505800-153509400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:153506000-153508000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:153506000-153508000	Transcr. at gene 5' and 3'	NHLF	lung
15	chr1:153506000-153508200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
16	chr1:153506000-153508400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
17	chr1:153506200-153508400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
18	chr1:153506400-153508000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:153506400-153508200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
20	chr1:153506600-153508000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:153506600-153508000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:153506600-153508000	Transcr. at gene 5' and 3'	HMEC	breast
23	chr1:153506600-153508000	Enhancers	K562	blood
24	chr1:153506600-153508200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr1:153506800-153508400	Transcr. at gene 5' and 3'	NHEK	skin
26	chr1:153506800-153509000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:153506800-153509200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr1:153507000-153508000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr1:153507000-153509200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:153507000-153509400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:153507200-153508000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr1:153507200-153508000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:153507200-153508000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:153507200-153508000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:153507200-153508000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:153507200-153508200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:153507200-153508200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:153507200-153509000	Flanking Active TSS	Spleen	Spleen
39	chr1:153507200-153509200	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr1:153507400-153508000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
41	chr1:153507400-153508000	Flanking Active TSS	Gastric	stomach
42	chr1:153507400-153508000	Flanking Active TSS	Lung	lung
43	chr1:153507400-153508000	Flanking Active TSS	Pancreas	Pancrea
44	chr1:153507400-153508200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr1:153507400-153508200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr1:153507400-153508200	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr1:153507400-153508200	Flanking Active TSS	Hela-S3	cervix
48	chr1:153507400-153508400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr1:153507400-153508400	Flanking Active TSS	Right Ventricle	heart
50	chr1:153507400-153509400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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