Variant report

Variant	rs17559050
Chromosome Location	chr1:224026445-224026446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224007285..224009204-chr1:224024898..224026701,2	K562	blood:
2	chr1:224021776..224023617-chr1:224025728..224028035,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10799327	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915882	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915892	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915917	0.95[EUR][1000 genomes]
rs10915946	0.91[EUR][1000 genomes]
rs10915948	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10915950	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10915956	0.91[EUR][1000 genomes]
rs1124943	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11801971	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11802505	0.92[EUR][1000 genomes]
rs11806886	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12021759	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12021785	0.95[EUR][1000 genomes]
rs12024535	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12026098	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12026835	0.95[EUR][1000 genomes]
rs12027539	0.95[EUR][1000 genomes]
rs12030094	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12038299	0.87[EUR][1000 genomes]
rs12040633	0.89[EUR][1000 genomes]
rs12042503	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12045776	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12730520	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12731254	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12745879	0.88[EUR][1000 genomes]
rs12747926	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17559134	0.91[ASN][1000 genomes]
rs17599	0.83[EUR][1000 genomes]
rs2014441	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2126389	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2169459	0.93[EUR][1000 genomes]
rs34124959	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35634773	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856161	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653644	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653645	0.95[EUR][1000 genomes]
rs4653775	0.83[EUR][1000 genomes]
rs56280097	0.91[EUR][1000 genomes]
rs59866505	0.89[EUR][1000 genomes]
rs61823593	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61823594	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61823595	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61824002	0.86[EUR][1000 genomes]
rs61824006	0.81[EUR][1000 genomes]
rs6658752	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6677956	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6678103	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6688246	0.95[EUR][1000 genomes]
rs6693324	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6702843	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs723999	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs745697	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7516059	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7519753	0.95[EUR][1000 genomes]
rs7533614	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7554109	0.95[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	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224017600-224026800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:224019400-224027000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr1:224019600-224027400	Enhancers	Fetal Heart	heart
4	chr1:224019800-224026600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:224020800-224028600	Weak transcription	Placenta	Placenta
7	chr1:224020800-224031600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:224021200-224027000	Enhancers	Brain Substantia Nigra	brain
9	chr1:224021400-224027000	Enhancers	Fetal Lung	lung
10	chr1:224022400-224026600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:224022800-224026800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:224023000-224026800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:224023000-224027000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:224023000-224029000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:224023000-224030600	Weak transcription	Fetal Kidney	kidney
16	chr1:224023200-224026600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:224023200-224031600	Weak transcription	Hela-S3	cervix
18	chr1:224023400-224026600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:224023400-224026600	Enhancers	Left Ventricle	heart
20	chr1:224023400-224026600	Enhancers	Dnd41	blood
21	chr1:224023400-224027000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:224023400-224027400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:224023600-224027000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:224023800-224026600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:224023800-224026600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:224023800-224026600	Enhancers	Right Ventricle	heart
27	chr1:224023800-224027000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:224023800-224028000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:224024000-224026600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:224024000-224027800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:224024000-224028000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:224024000-224031800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:224024000-224031800	Weak transcription	Thymus	Thymus
34	chr1:224024200-224027000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:224024200-224027200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:224024200-224028000	Weak transcription	NHDF-Ad	bronchial
37	chr1:224024200-224031600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:224024200-224031600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:224024200-224031800	Weak transcription	Adipose Nuclei	Adipose
41	chr1:224024400-224026600	Enhancers	Fetal Muscle Leg	muscle
42	chr1:224024400-224026800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:224024400-224031800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:224024600-224028800	Weak transcription	Psoas Muscle	Psoas
45	chr1:224024600-224029600	Weak transcription	Pancreas	Pancrea
46	chr1:224024600-224030800	Weak transcription	Primary B cells from cord blood	blood
47	chr1:224024600-224031600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:224024600-224031800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:224024600-224031800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:224024600-224031800	Weak transcription	Brain Cingulate Gyrus	brain

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