Variant report

Variant	rs590825
Chromosome Location	chr1:120287800-120287801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120286920..120290208-chr1:120298529..120301740,3	K562	blood:
2	chr1:120261924..120264165-chr1:120287525..120289595,2	K562	blood:
3	chr1:120278483..120280232-chr1:120286168..120288570,2	K562	blood:
4	chr1:120286100..120288877-chr1:120290549..120293981,3	K562	blood:
5	chr1:120278363..120280873-chr1:120284153..120287954,3	K562	blood:
6	chr1:120281250..120283814-chr1:120284593..120287866,3	K562	blood:
7	chr1:120286505..120288307-chr1:120292207..120294976,2	K562	blood:
8	chr1:120282346..120286075-chr1:120287322..120291391,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1441008	0.82[CHB][hapmap]
rs1441010	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs518027	0.87[CEU][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs522277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543703	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566864	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs591162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608358	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs610404	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs627070	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs649733	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667246	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689198	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
6	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:120262000-120287800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:120262000-120288200	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr1:120262400-120288200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:120279200-120290600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:120280400-120289400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:120282000-120293400	Weak transcription	Aorta	Aorta
10	chr1:120283600-120288600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:120284000-120288000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:120284400-120287800	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr1:120285200-120287800	Genic enhancers	Fetal Intestine Small	intestine
14	chr1:120285400-120288800	Weak transcription	HSMM	muscle
15	chr1:120285600-120292200	Weak transcription	Lung	lung
16	chr1:120285800-120289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:120285800-120289600	Weak transcription	Ovary	ovary
18	chr1:120286000-120288600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:120286000-120289600	Weak transcription	Pancreas	Pancrea
20	chr1:120286000-120290000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:120286000-120290200	Weak transcription	NHLF	lung
22	chr1:120286200-120289200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:120286200-120289200	Weak transcription	Placenta	Placenta
24	chr1:120286400-120288200	Weak transcription	Thymus	Thymus
25	chr1:120286400-120289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:120286600-120288200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:120286600-120289200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:120286600-120289200	Weak transcription	Gastric	stomach
29	chr1:120286600-120289200	Weak transcription	HMEC	breast
30	chr1:120286600-120289600	Enhancers	Liver	Liver
31	chr1:120286600-120289600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:120286600-120291400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:120286800-120288200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:120286800-120288200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:120286800-120288400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:120286800-120288600	Weak transcription	Primary T cells from cord blood	blood
37	chr1:120286800-120288600	Enhancers	HepG2	liver
38	chr1:120286800-120289600	Weak transcription	Esophagus	oesophagus
39	chr1:120286800-120289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:120286800-120289800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:120286800-120290800	Weak transcription	Adipose Nuclei	Adipose
42	chr1:120286800-120290800	Weak transcription	Colonic Mucosa	Colon
43	chr1:120286800-120290800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:120286800-120290800	Weak transcription	Fetal Lung	lung
45	chr1:120286800-120297800	Weak transcription	Right Ventricle	heart
46	chr1:120286800-120302200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
48	chr1:120287000-120288000	Enhancers	Fetal Stomach	stomach
49	chr1:120287000-120288200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:120287000-120290800	Weak transcription	Spleen	Spleen

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