Variant report

Variant	rs59533551
Chromosome Location	chr1:9960385-9960386
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9960360..9963162-chr1:10094643..10096453,2	K562	blood:
2	chr1:9959637..9962157-chr1:10000997..10004745,4	K562	blood:
3	chr1:9959497..9963763-chr1:9965322..9971774,8	K562	blood:
4	chr1:9950605..9953438-chr1:9958773..9961465,2	MCF-7	breast:
5	chr1:9958976..9964207-chr1:9967620..9971774,11	K562	blood:
6	chr1:9958455..9962584-chr1:9963252..9967560,5	MCF-7	breast:
7	chr1:9943285..9945360-chr1:9959805..9962322,3	K562	blood:
8	chr1:9959445..9961171-chr1:9968513..9970561,2	MCF-7	breast:
9	chr1:9958629..9960464-chr1:9968400..9970687,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11121499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11809921	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1220408	0.93[ASN][1000 genomes]
rs15177	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17034420	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033960	0.86[EUR][1000 genomes]
rs2278611	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3860318	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3888014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56315207	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57979292	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58281392	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59341676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59530761	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60389428	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60547803	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60624175	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61785229	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61785586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61785590	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658583	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6683824	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6695334	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72858068	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74054138	0.85[AMR][1000 genomes]
rs7529783	0.85[AMR][1000 genomes]
rs7533225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9935600-9960800	Weak transcription	Fetal Intestine Large	intestine
2	chr1:9943200-9961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:9943600-9960800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:9949400-9967600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:9950600-9960600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:9951200-9960600	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:9951200-9961600	Weak transcription	Fetal Brain Female	brain
8	chr1:9951400-9962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:9951600-9961800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:9951600-9969000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:9951800-9960400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:9951800-9960600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:9953000-9960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:9953400-9960400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:9953600-9960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:9953600-9960400	Weak transcription	Right Ventricle	heart
17	chr1:9953600-9960600	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:9953600-9961200	Weak transcription	Gastric	stomach
19	chr1:9953800-9960600	Weak transcription	Primary B cells from cord blood	blood
20	chr1:9954000-9964600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:9954400-9960600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:9954400-9960600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:9954600-9960400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:9954600-9960400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:9954600-9960400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:9954600-9961400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:9954600-9961600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:9954800-9960400	Weak transcription	Spleen	Spleen
29	chr1:9954800-9960600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:9955000-9960600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:9957800-9960600	Enhancers	Left Ventricle	heart
32	chr1:9958000-9968800	Weak transcription	Fetal Stomach	stomach
33	chr1:9958600-9960600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:9958800-9960400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:9958800-9969000	Weak transcription	Hela-S3	cervix
36	chr1:9959000-9960600	Weak transcription	HMEC	breast
37	chr1:9959000-9960800	Weak transcription	HSMM	muscle
38	chr1:9959000-9964400	Weak transcription	HSMMtube	muscle
39	chr1:9959000-9964400	Weak transcription	NH-A	brain
40	chr1:9959000-9964800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:9959200-9960400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:9959600-9963800	Enhancers	Stomach Mucosa	stomach
43	chr1:9959800-9960400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:9959800-9962800	Enhancers	Lung	lung
45	chr1:9960000-9960400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:9960000-9960400	Enhancers	Brain Angular Gyrus	brain
47	chr1:9960000-9960400	Enhancers	Brain Anterior Caudate	brain
48	chr1:9960000-9960400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:9960000-9960400	Enhancers	Brain Substantia Nigra	brain
50	chr1:9960000-9960400	Enhancers	Duodenum Mucosa	Duodenum

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