Variant report

Variant	rs60660559
Chromosome Location	chr1:46029317-46029318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46014232..46017206-chr1:46025290..46030299,5	K562	blood:
2	chr1:46016398..46018612-chr1:46028502..46030391,2	MCF-7	breast:
3	chr1:46027383..46031595-chr1:46048142..46051631,6	K562	blood:
4	chr1:46021617..46024409-chr1:46027059..46029406,2	K562	blood:
5	chr1:45982318..45989250-chr1:46023024..46029715,13	K562	blood:
6	chr1:46015633..46018049-chr1:46028799..46031573,2	K562	blood:
7	chr1:46026984..46033199-chr1:46047562..46051151,12	K562	blood:

Variant related genes	Relation type
ENSG00000132780	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11211125	1.00[EUR][1000 genomes]
rs11211127	1.00[EUR][1000 genomes]
rs12065695	1.00[EUR][1000 genomes]
rs12066809	1.00[EUR][1000 genomes]
rs12067882	1.00[EUR][1000 genomes]
rs12070890	1.00[EUR][1000 genomes]
rs12073047	1.00[EUR][1000 genomes]
rs12083690	1.00[EUR][1000 genomes]
rs12091335	1.00[EUR][1000 genomes]
rs12093444	1.00[EUR][1000 genomes]
rs16832540	1.00[EUR][1000 genomes]
rs16832545	1.00[EUR][1000 genomes]
rs16832550	1.00[EUR][1000 genomes]
rs16832557	1.00[EUR][1000 genomes]
rs16832559	1.00[EUR][1000 genomes]
rs1855621	1.00[EUR][1000 genomes]
rs28532613	1.00[EUR][1000 genomes]
rs2934860	1.00[EUR][1000 genomes]
rs2934861	1.00[EUR][1000 genomes]
rs2934863	1.00[EUR][1000 genomes]
rs2934864	1.00[EUR][1000 genomes]
rs2991967	1.00[EUR][1000 genomes]
rs2991969	1.00[EUR][1000 genomes]
rs2991984	1.00[EUR][1000 genomes]
rs2993256	1.00[EUR][1000 genomes]
rs2993260	1.00[EUR][1000 genomes]
rs2993261	1.00[EUR][1000 genomes]
rs3014222	1.00[EUR][1000 genomes]
rs3014223	1.00[EUR][1000 genomes]
rs3014224	1.00[EUR][1000 genomes]
rs3014226	1.00[EUR][1000 genomes]
rs35067820	1.00[EUR][1000 genomes]
rs35103566	1.00[EUR][1000 genomes]
rs36053912	1.00[EUR][1000 genomes]
rs57910611	1.00[EUR][1000 genomes]
rs59050426	1.00[EUR][1000 genomes]
rs60189617	1.00[AMR][1000 genomes]
rs60199320	1.00[AMR][1000 genomes]
rs60347972	1.00[EUR][1000 genomes]
rs60916630	1.00[AMR][1000 genomes]
rs60952228	0.84[AFR][1000 genomes]
rs6664588	1.00[EUR][1000 genomes]
rs6671347	1.00[EUR][1000 genomes]
rs6677135	1.00[EUR][1000 genomes]
rs6699702	1.00[EUR][1000 genomes]
rs72896187	1.00[EUR][1000 genomes]
rs72898313	1.00[EUR][1000 genomes]
rs72898315	1.00[EUR][1000 genomes]
rs72898320	1.00[EUR][1000 genomes]
rs72898323	1.00[EUR][1000 genomes]
rs72900311	1.00[EUR][1000 genomes]
rs7412911	1.00[EUR][1000 genomes]
rs7536559	1.00[EUR][1000 genomes]
rs7550744	1.00[EUR][1000 genomes]
rs9429080	1.00[EUR][1000 genomes]
rs9429083	1.00[EUR][1000 genomes]
rs9429164	1.00[EUR][1000 genomes]
rs9429165	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 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	chr1:46017800-46032200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:46018000-46032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:46018400-46029600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:46018400-46029800	Weak transcription	NHDF-Ad	bronchial
8	chr1:46018400-46032000	Weak transcription	Fetal Kidney	kidney
9	chr1:46018400-46032600	Weak transcription	Fetal Brain Male	brain
10	chr1:46018400-46036400	Strong transcription	Fetal Stomach	stomach
11	chr1:46018400-46036800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:46018400-46036800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:46018400-46036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:46018400-46037000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:46018600-46032000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:46018600-46034200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:46018600-46036800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:46018600-46037600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:46018600-46038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:46019200-46032000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:46020600-46032200	Weak transcription	Brain Angular Gyrus	brain
22	chr1:46021600-46029600	Weak transcription	HSMM	muscle
23	chr1:46022000-46032200	Weak transcription	NHLF	lung
24	chr1:46022800-46030400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:46022800-46036800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:46023000-46030200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:46023000-46036600	Strong transcription	Dnd41	blood
28	chr1:46023400-46030600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:46023400-46032000	Weak transcription	Pancreas	Pancrea
30	chr1:46023400-46032200	Weak transcription	Right Atrium	heart
31	chr1:46023400-46032600	Weak transcription	Small Intestine	intestine
32	chr1:46023400-46037200	Weak transcription	Psoas Muscle	Psoas
33	chr1:46023600-46032000	Weak transcription	Fetal Heart	heart
34	chr1:46023600-46032200	Weak transcription	HMEC	breast
35	chr1:46023600-46032400	Weak transcription	Stomach Mucosa	stomach
36	chr1:46023800-46032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:46024400-46030400	Strong transcription	Fetal Brain Female	brain
38	chr1:46024400-46030600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:46024400-46030600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:46024400-46037200	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:46024600-46036800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:46024800-46029400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:46024800-46030400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:46025200-46032200	Weak transcription	Hela-S3	cervix
45	chr1:46025400-46030200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:46025400-46030200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:46025600-46030400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:46025600-46030400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:46025800-46030200	Strong transcription	Placenta	Placenta
50	chr1:46025800-46030200	Strong transcription	Spleen	Spleen

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