Variant report

Variant	rs28880007
Chromosome Location	chr7:6159067-6159068
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	chr7:6141805..6147526-chr7:6152442..6159269,12	MCF-7	breast:
2	chr7:6151184..6155498-chr7:6158937..6162352,4	K562	blood:

Variant related genes	Relation type
ENSG00000106346	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10046499	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10216107	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10225119	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10226743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10228389	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10228430	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10242394	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10246266	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10250285	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10254689	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10255598	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10255914	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10255918	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10257181	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10257248	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10257654	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10257971	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10261466	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10275021	0.84[ASN][1000 genomes]
rs10279137	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10280585	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10282278	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11768047	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11770730	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12667323	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12667392	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13437890	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17136048	0.84[ASN][1000 genomes]
rs28385378	0.89[ASN][1000 genomes]
rs28575447	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28589289	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28758696	0.82[AMR][1000 genomes]
rs60892137	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61750868	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61753115	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61753118	0.92[EUR][1000 genomes]
rs6944071	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6949823	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7796322	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9655493	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
3	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
5	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
7	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
8	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	127 gene(s)	inside rSNPs	diseases
9	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
10	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
11	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
12	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 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	chr7:6145600-6186000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:6145600-6186400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:6146400-6159400	Weak transcription	Gastric	stomach
4	chr7:6146400-6159800	Weak transcription	Pancreas	Pancrea
5	chr7:6146800-6218200	Weak transcription	Stomach Mucosa	stomach
6	chr7:6149200-6160000	Strong transcription	Fetal Stomach	stomach
7	chr7:6149400-6159800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:6149600-6159800	Strong transcription	Fetal Intestine Small	intestine
9	chr7:6149800-6159800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:6150400-6160200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:6150600-6159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:6150600-6159400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr7:6150600-6159600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:6150600-6159800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr7:6150600-6160600	Strong transcription	Primary T cells from cord blood	blood
16	chr7:6150600-6160800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:6150600-6160800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr7:6150600-6162000	Strong transcription	Osteobl	bone
19	chr7:6150600-6162800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:6150600-6163800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:6150600-6166000	Strong transcription	HepG2	liver
22	chr7:6150600-6171400	Strong transcription	Dnd41	blood
23	chr7:6150800-6159400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:6150800-6159800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:6150800-6160000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:6150800-6160200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:6150800-6160400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:6150800-6160600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:6150800-6161800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr7:6150800-6163600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:6150800-6165200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:6151000-6160200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:6151000-6165000	Strong transcription	Placenta	Placenta
34	chr7:6151200-6162600	Strong transcription	Left Ventricle	heart
35	chr7:6151600-6159800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:6151800-6163600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr7:6152000-6159600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:6152000-6159600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:6152000-6160000	Strong transcription	Fetal Thymus	thymus
40	chr7:6152000-6160200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:6152000-6160800	Strong transcription	Fetal Lung	lung
42	chr7:6152200-6159800	Strong transcription	HSMM	muscle
43	chr7:6152200-6160200	Strong transcription	Adipose Nuclei	Adipose
44	chr7:6152200-6163000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:6152400-6160800	Strong transcription	Brain Anterior Caudate	brain
46	chr7:6152600-6159200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr7:6152800-6159600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr7:6152800-6159600	Strong transcription	K562	blood
49	chr7:6153200-6163800	Strong transcription	Lung	lung
50	chr7:6154600-6159800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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