Variant report

Variant	rs6428390
Chromosome Location	chr1:197159112-197159113
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197148315..197153030-chr1:197158427..197161690,6	K562	blood:
2	chr1:197158202..197161289-chr1:197163593..197166561,4	MCF-7	breast:
3	chr1:197153871..197156046-chr1:197157510..197159147,2	K562	blood:
4	chr1:197155834..197158603-chr1:197158660..197160759,2	K562	blood:
5	chr1:197157362..197159719-chr1:197168800..197171686,3	K562	blood:

Variant related genes	Relation type
ENSG00000134376	Chromatin interaction
ENSG00000177888	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10429911	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10732295	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10732296	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10754219	0.95[EUR][1000 genomes]
rs10801593	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10801594	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1415217	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1556763	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1764629	0.86[EUR][1000 genomes]
rs1764800	0.83[EUR][1000 genomes]
rs4244141	1.00[EUR][1000 genomes]
rs4342879	0.94[AMR][1000 genomes]
rs476390	0.83[EUR][1000 genomes]
rs4915378	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4915379	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5029273	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs510135	0.89[EUR][1000 genomes]
rs518149	0.89[EUR][1000 genomes]
rs568757	0.83[EUR][1000 genomes]
rs571106	0.83[EUR][1000 genomes]
rs615647	0.89[EUR][1000 genomes]
rs616675	0.83[EUR][1000 genomes]
rs6701681	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7513826	0.97[EUR][1000 genomes]
rs7520503	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7523013	0.97[EUR][1000 genomes]
rs7554802	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7554890	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7554995	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873070	chr1:197079671-197165014	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv947366	chr1:197157398-197163669	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
3	chr1:197125600-197160000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
5	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:197128200-197161000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:197135200-197161800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:197136000-197161600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:197141400-197166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:197142000-197159600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr1:197142200-197159800	Strong transcription	Fetal Thymus	thymus
12	chr1:197143200-197165800	Weak transcription	Small Intestine	intestine
13	chr1:197147600-197161000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:197148400-197160800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:197148400-197161200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:197148600-197159600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:197148800-197161000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:197149800-197165400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:197151200-197160200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:197152000-197161000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:197152400-197161000	Strong transcription	Dnd41	blood
22	chr1:197152400-197168600	Weak transcription	Stomach Mucosa	stomach
23	chr1:197152800-197161600	Strong transcription	HSMM	muscle
24	chr1:197153200-197165000	Weak transcription	Fetal Heart	heart
25	chr1:197153400-197161000	Strong transcription	Primary B cells from cord blood	blood
26	chr1:197153400-197161000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:197154000-197160200	Strong transcription	Osteobl	bone
28	chr1:197154200-197159600	Strong transcription	Primary T cells from cord blood	blood
29	chr1:197154200-197159600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:197154200-197160800	Strong transcription	Fetal Lung	lung
31	chr1:197154200-197161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:197154200-197161000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:197154200-197161000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:197154200-197161000	Strong transcription	Liver	Liver
35	chr1:197154200-197161000	Strong transcription	Placenta	Placenta
36	chr1:197154200-197161400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:197154400-197159200	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr1:197154400-197159600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:197154400-197159600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:197154400-197159600	Strong transcription	Adipose Nuclei	Adipose
41	chr1:197154400-197159800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:197154400-197160000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:197154400-197160200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:197154400-197160200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:197154400-197160200	Strong transcription	Brain Anterior Caudate	brain
46	chr1:197154400-197160600	Strong transcription	Fetal Intestine Large	intestine
47	chr1:197154400-197160800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:197154400-197161000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:197154400-197161200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:197154400-197161200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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