Variant report

Variant	rs56859218
Chromosome Location	chr1:169349914-169349915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169346482..169351680-chr1:169353078..169360345,13	K562	blood:
2	chr1:169341801..169344771-chr1:169346777..169350780,3	MCF-7	breast:
3	chr1:169346112..169350144-chr1:169384504..169386593,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10489187	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489188	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919146	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10919155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919163	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799936	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11799948	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11808015	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11809378	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12021770	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023025	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023117	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023892	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026728	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12028813	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030320	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033253	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12049227	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12239720	0.81[ASN][1000 genomes]
rs1400838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16862118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862172	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2235195	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28566091	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35269183	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807018	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808977	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61808978	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61808980	0.81[ASN][1000 genomes]
rs6427191	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72702156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72702179	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72702188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535788	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554703	0.97[ASN][1000 genomes]
rs9659035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	56 gene(s)	inside rSNPs	diseases
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169351200	Weak transcription	Lung	lung
2	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
3	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
4	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
5	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
6	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:169338000-169365200	Weak transcription	Gastric	stomach
8	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
9	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
15	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
19	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
20	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
21	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:169339200-169351800	Weak transcription	Fetal Brain Male	brain
25	chr1:169339600-169351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:169340200-169356400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:169340400-169366000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:169341000-169351400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:169342800-169351200	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:169343000-169351400	Weak transcription	K562	blood
32	chr1:169344200-169360200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:169344800-169359200	Strong transcription	HSMM	muscle
34	chr1:169344800-169361200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:169344800-169362600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:169344800-169365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:169345000-169355400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:169345000-169360800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:169345000-169366000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:169345200-169352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:169345200-169352400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:169345200-169353600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:169345400-169353600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:169345400-169354000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:169345400-169366000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:169345600-169352400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:169345600-169352800	Strong transcription	HUVEC	blood vessel
48	chr1:169345600-169355000	Strong transcription	A549	lung
49	chr1:169345600-169360800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:169345600-169366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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