Variant report

Variant	rs59517508
Chromosome Location	chr1:45770144-45770145
allele	A/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:49)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:49 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45767756..45770451-chr1:45964648..45967377,2	K562	blood:
2	chr1:45769529..45771862-chr1:45787888..45789985,2	K562	blood:
3	chr1:45768281..45771138-chr1:45796764..45802126,5	MCF-7	breast:
4	chr1:45768003..45772070-chr1:45964648..45967315,5	K562	blood:
5	chr1:45276358..45278669-chr1:45768111..45770170,2	K562	blood:
6	chr1:45767877..45774853-chr1:45802459..45807372,12	K562	blood:
7	chr1:45768778..45770892-chr1:45955419..45957288,2	MCF-7	breast:
8	chr1:45239714..45242119-chr1:45768024..45770641,2	K562	blood:
9	chr1:45271518..45274084-chr1:45769470..45771015,2	K562	blood:
10	chr1:45196186..45198352-chr1:45768360..45771059,2	MCF-7	breast:
11	chr1:45769560..45771577-chr1:45812920..45815177,2	K562	blood:
12	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
13	chr1:45767832..45771484-chr1:45985093..45988810,5	K562	blood:
14	chr1:45770114..45770815-chr1:45982208..45983001,2	MCF-7	breast:
15	chr1:45262923..45267744-chr1:45767225..45772183,8	K562	blood:
16	chr1:45240455..45242747-chr1:45769407..45771575,2	K562	blood:
17	chr1:45450947..45453129-chr1:45770139..45772507,2	K562	blood:
18	chr1:45184077..45189466-chr1:45767737..45771248,11	K562	blood:
19	chr1:45293029..45295076-chr1:45769453..45771554,2	MCF-7	breast:
20	chr1:45756933..45758729-chr1:45768463..45770390,2	K562	blood:
21	chr1:45284161..45290157-chr1:45766666..45771483,12	K562	blood:
22	chr1:45767853..45771862-chr1:45786144..45789985,4	K562	blood:
23	chr1:45194559..45197105-chr1:45768008..45770693,4	K562	blood:
24	chr1:45768158..45770163-chr1:45795401..45797079,2	K562	blood:
25	chr1:45769352..45770932-chr19:13264872..13267735,2	K562	blood:
26	chr1:45283674..45286034-chr1:45767652..45771171,5	MCF-7	breast:
27	chr1:45396788..45398380-chr1:45768568..45771235,2	K562	blood:
28	chr1:45264001..45267369-chr1:45768099..45771014,4	K562	blood:
29	chr1:45479863..45480810-chr1:45768917..45770306,5	K562	blood:
30	chr1:45193680..45198999-chr1:45768008..45771912,9	K562	blood:
31	chr1:45185975..45188981-chr1:45767504..45771091,13	K562	blood:
32	chr1:45735419..45737073-chr1:45768258..45770509,2	K562	blood:
33	chr1:45276358..45279263-chr1:45768111..45771018,3	K562	blood:
34	chr1:45282609..45288514-chr1:45767803..45773154,13	K562	blood:
35	chr1:45768289..45770936-chr1:45808529..45810402,2	K562	blood:
36	chr1:45769536..45771577-chr1:45812790..45815177,2	K562	blood:
37	chr1:45769704..45770325-chr20:61427142..61427771,2	Hela-S3	cervix:
38	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:
39	chr1:45769724..45771289-chr1:45824669..45826392,2	MCF-7	breast:
40	chr1:45768110..45772204-chr1:45801230..45805942,7	MCF-7	breast:
41	chr1:45767776..45771231-chr1:45801954..45807210,10	K562	blood:
42	chr1:45484129..45484961-chr1:45769347..45770315,2	K562	blood:
43	chr1:45770100..45770928-chr1:45795035..45795616,2	MCF-7	breast:
44	chr1:45296461..45296968-chr1:45769169..45770161,3	K562	blood:
45	chr1:45763746..45766388-chr1:45768053..45771001,2	MCF-7	breast:
46	chr1:45476329..45477906-chr1:45768337..45771148,2	MCF-7	breast:
47	chr1:45768893..45771768-chr1:45791455..45796830,6	MCF-7	breast:
48	chr1:45761109..45763795-chr1:45769192..45770940,3	K562	blood:
49	chr1:45767740..45770966-chr1:46047969..46050912,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUTYH-1	chr1:45769863-45770750	ENSG00000246279
2	lnc-HPDL-2	chr1:45769582-45771291	NONHSAT002925

No data

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000186603	Chromatin interaction
ENSG00000253039	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000267598	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11810682	1.00[ASN][1000 genomes]
rs1691220	1.00[AMR][1000 genomes]
rs72478599	0.93[ASN][1000 genomes]
rs72890555	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521364	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7555357	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs781228	1.00[AMR][1000 genomes]
rs781229	1.00[AMR][1000 genomes]
rs9429064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45768400-45770200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:45768400-45770200	Active TSS	Brain Substantia Nigra	brain
3	chr1:45768400-45770400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:45768600-45770200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:45768600-45770200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:45768600-45770200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:45768600-45770200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:45768600-45770200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:45768600-45770200	Active TSS	Right Ventricle	heart
10	chr1:45768600-45770400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:45768600-45770400	Active TSS	Fetal Kidney	kidney
12	chr1:45768600-45770400	Active TSS	Psoas Muscle	Psoas
13	chr1:45768600-45770400	Active TSS	HepG2	liver
14	chr1:45768600-45770600	Active TSS	HSMM	muscle
15	chr1:45768800-45770200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:45768800-45770200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:45768800-45770200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:45768800-45770200	Active TSS	Aorta	Aorta
19	chr1:45768800-45770200	Active TSS	Brain Angular Gyrus	brain
20	chr1:45768800-45770200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:45768800-45770200	Active TSS	Esophagus	oesophagus
22	chr1:45768800-45770200	Active TSS	Fetal Heart	heart
23	chr1:45768800-45770200	Active TSS	Ovary	ovary
24	chr1:45768800-45770200	Active TSS	Small Intestine	intestine
25	chr1:45768800-45770200	Active TSS	GM12878-XiMat	blood
26	chr1:45768800-45770400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:45768800-45770400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:45768800-45770400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:45768800-45770400	Active TSS	Pancreas	Pancrea
30	chr1:45769000-45770200	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr1:45769600-45770200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:45769600-45770200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:45769600-45770400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:45769600-45770600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:45769600-45770600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr1:45769600-45770800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr1:45769800-45770200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:45769800-45770200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:45769800-45770200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:45769800-45770200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr1:45769800-45770200	Flanking Active TSS	Placenta	Placenta
42	chr1:45769800-45770200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr1:45769800-45770200	Flanking Active TSS	Spleen	Spleen
44	chr1:45769800-45770200	Flanking Active TSS	HUVEC	blood vessel
45	chr1:45769800-45770400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr1:45769800-45770400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr1:45769800-45770400	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr1:45769800-45770400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr1:45769800-45770400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr1:45769800-45770400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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