Variant report

Variant	rs1929859
Chromosome Location	chr1:227218664-227218665
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	chr1:227203735..227207189-chr1:227216806..227218910,3	K562	blood:
2	chr1:227216665..227219394-chr1:227921032..227923176,2	K562	blood:

Variant related genes	Relation type
ENSG00000081692	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10458379	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916098	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12035998	0.82[ASN][1000 genomes]
rs12080452	0.81[ASN][1000 genomes]
rs12095674	0.82[ASN][1000 genomes]
rs12097121	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2104863	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2458523	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482453	1.00[ASN][1000 genomes]
rs4551562	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653477	0.82[ASN][1000 genomes]
rs4653788	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653790	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477373	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482032	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533134	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567467	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58442036	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs595155	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61834563	0.82[ASN][1000 genomes]
rs61836477	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645081	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664803	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688718	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536444	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs871210	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1007352	chr1:227196502-227247160	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997751	chr1:227196502-227263537	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1010864	chr1:227199493-227246753	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014423	chr1:227201253-227268843	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
3	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
4	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
6	chr1:227183200-227228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227183200-227240400	Weak transcription	Colonic Mucosa	Colon
8	chr1:227184000-227234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:227190600-227223200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:227190600-227272600	Weak transcription	Lung	lung
11	chr1:227192600-227220200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:227192800-227220200	Weak transcription	Gastric	stomach
13	chr1:227202600-227222600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
15	chr1:227205600-227220400	Weak transcription	Stomach Mucosa	stomach
16	chr1:227207600-227242000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:227208800-227222600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:227209000-227231000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:227209000-227234600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
21	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:227209800-227222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:227210200-227226400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:227210600-227245800	Weak transcription	NHEK	skin
25	chr1:227212200-227223000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:227212800-227226400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:227213000-227219200	Strong transcription	Liver	Liver
28	chr1:227213200-227222400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:227213400-227220000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:227213600-227228000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:227213800-227222000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:227214000-227220800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:227214000-227222600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:227214200-227220200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:227214600-227221600	Weak transcription	Fetal Heart	heart
36	chr1:227214600-227226200	Weak transcription	Brain Germinal Matrix	brain
37	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
38	chr1:227215000-227222400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:227215200-227220000	Weak transcription	Aorta	Aorta
40	chr1:227215400-227219000	Strong transcription	HMEC	breast
41	chr1:227215600-227230400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:227216200-227219600	Strong transcription	NH-A	brain
43	chr1:227216200-227220400	Strong transcription	NHDF-Ad	bronchial
44	chr1:227216600-227226400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:227216800-227218800	Weak transcription	Brain Anterior Caudate	brain
46	chr1:227216800-227218800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:227216800-227220000	Weak transcription	Fetal Lung	lung
48	chr1:227216800-227220000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:227216800-227221400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:227216800-227221400	Weak transcription	Ovary	ovary

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