Variant report

Variant	rs59404931
Chromosome Location	chr1:227839550-227839551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227833022..227835351-chr1:227838845..227841426,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12563564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12564917	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12565618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12565653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12567084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16847912	1.00[AMR][1000 genomes]
rs16847929	1.00[AMR][1000 genomes]
rs16847987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16859962	1.00[AMR][1000 genomes]
rs16860227	1.00[AMR][1000 genomes]
rs17492447	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2101862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2313220	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35703429	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57165550	1.00[AMR][1000 genomes]
rs58322371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59461077	1.00[AMR][1000 genomes]
rs59772630	1.00[AMR][1000 genomes]
rs60835672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61283390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6665512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6675470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73088936	1.00[AMR][1000 genomes]
rs73090912	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090935	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090936	1.00[AMR][1000 genomes]
rs73090937	1.00[AMR][1000 genomes]
rs73090938	1.00[AMR][1000 genomes]
rs73090942	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090947	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090948	1.00[AMR][1000 genomes]
rs73090952	1.00[AMR][1000 genomes]
rs73090959	1.00[AMR][1000 genomes]
rs73090985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090986	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090987	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090994	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73091000	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092610	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092646	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093304	1.00[AMR][1000 genomes]
rs73093319	1.00[AMR][1000 genomes]
rs73093328	1.00[AMR][1000 genomes]
rs73093344	1.00[AMR][1000 genomes]
rs73093354	1.00[AMR][1000 genomes]
rs73094528	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094566	1.00[AFR][1000 genomes]
rs73094571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73098926	1.00[AMR][1000 genomes]
rs73098933	1.00[AMR][1000 genomes]
rs73099300	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099302	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73101625	1.00[AMR][1000 genomes]
rs73101653	1.00[AMR][1000 genomes]
rs7526436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546845	1.00[AMR][1000 genomes]
rs7554851	1.00[AMR][1000 genomes]
rs7554870	1.00[AMR][1000 genomes]
rs7555208	1.00[AMR][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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227820600-227861600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr1:227827800-227845400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
4	chr1:227829400-227859800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:227830800-227845200	ZNF genes & repeats	Dnd41	blood
6	chr1:227831800-227839800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr1:227831800-227840000	ZNF genes & repeats	Primary B cells from cord blood	blood
8	chr1:227831800-227850200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
9	chr1:227831800-227851600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:227831800-227854600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr1:227831800-227864000	ZNF genes & repeats	Liver	Liver
12	chr1:227832000-227843600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
13	chr1:227832000-227845200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr1:227832000-227850200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr1:227832000-227854400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr1:227832200-227850600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:227832400-227850400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr1:227832600-227846400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr1:227833400-227849600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr1:227834000-227839600	ZNF genes & repeats	Brain Anterior Caudate	brain
21	chr1:227834000-227843800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr1:227834000-227847200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:227835000-227852200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:227835000-227852600	ZNF genes & repeats	Fetal Brain Female	brain
25	chr1:227835200-227845200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
26	chr1:227835200-227847800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
27	chr1:227836400-227852200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr1:227837000-227839600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:227837000-227845000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
30	chr1:227838000-227839600	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
31	chr1:227838400-227839600	ZNF genes & repeats	Brain Hippocampus Middle	brain
32	chr1:227838400-227839600	ZNF genes & repeats	Fetal Lung	lung
33	chr1:227838400-227839800	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr1:227838400-227846600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:227838600-227839600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:227838600-227839600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:227838600-227839600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
38	chr1:227838600-227839600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr1:227838600-227839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:227838600-227839600	ZNF genes & repeats	Psoas Muscle	Psoas
41	chr1:227838600-227839600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
42	chr1:227838600-227839600	ZNF genes & repeats	HSMMtube	muscle
43	chr1:227838600-227839800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr1:227838600-227843400	ZNF genes & repeats	Colon Smooth Muscle	Colon
45	chr1:227838600-227843600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr1:227838600-227843600	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr1:227838600-227843800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:227838600-227845400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:227838600-227845400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
50	chr1:227838600-227847200	ZNF genes & repeats	Brain Substantia Nigra	brain

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