Variant report

Variant	rs28820905
Chromosome Location	chr7:98965658-98965659
allele	A/G
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	chr7:98964264..98966254-chr7:98968520..98970392,2	K562	blood:
2	chr7:98963718..98966584-chr7:99003795..99005637,2	MCF-7	breast:
3	chr7:98964521..98966549-chr7:98972530..98974086,2	K562	blood:
4	chr7:98963291..98965868-chr7:99006245..99008674,2	MCF-7	breast:
5	chr7:98965122..98966630-chr7:98972244..98974345,2	K562	blood:
6	chr7:98965082..98967314-chr7:98975254..98977961,2	K562	blood:
7	chr7:98888221..98890388-chr7:98963872..98966466,2	K562	blood:
8	chr7:98959822..98968172-chr7:98968902..98974586,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106245	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10155966	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10225529	0.87[EUR][1000 genomes]
rs10232076	0.86[ASN][1000 genomes]
rs10236149	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10243678	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249167	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255399	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10258757	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10267346	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10270459	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270917	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10272998	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10274407	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10953287	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11762273	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11973460	0.80[AMR][1000 genomes]
rs17161692	0.86[ASN][1000 genomes]
rs17161695	0.87[EUR][1000 genomes]
rs2072181	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2107922	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2286162	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301889	0.85[ASN][1000 genomes]
rs2404323	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28468623	0.85[ASN][1000 genomes]
rs28495024	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3801288	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58660994	0.85[ASN][1000 genomes]
rs59725656	0.85[ASN][1000 genomes]
rs6943920	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948775	0.86[ASN][1000 genomes]
rs6953476	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6955490	0.82[EUR][1000 genomes]
rs6972337	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6975099	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73395547	0.85[ASN][1000 genomes]
rs73395557	0.85[ASN][1000 genomes]
rs73395580	0.86[ASN][1000 genomes]
rs9641253	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9768020	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9918551	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28820905	ARPC1B	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:98928400-98967200	Strong transcription	Fetal Thymus	thymus
4	chr7:98930000-98968200	Strong transcription	Fetal Intestine Small	intestine
5	chr7:98930200-98968400	Strong transcription	Fetal Stomach	stomach
6	chr7:98930800-98966800	Strong transcription	Adipose Nuclei	Adipose
7	chr7:98930800-98967000	Strong transcription	Fetal Muscle Leg	muscle
8	chr7:98930800-98967600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr7:98932600-98966400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:98935600-98971600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:98944200-98967200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr7:98946400-98967600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr7:98951000-98967000	Strong transcription	Left Ventricle	heart
14	chr7:98953400-98967200	Strong transcription	Rectal Smooth Muscle	rectum
15	chr7:98953800-98971600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:98955000-98971600	Weak transcription	Right Atrium	heart
17	chr7:98955600-98970200	Weak transcription	Fetal Brain Male	brain
18	chr7:98956000-98966800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:98956200-98970400	Weak transcription	Stomach Mucosa	stomach
20	chr7:98956600-98967200	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr7:98957000-98966600	Strong transcription	Brain Hippocampus Middle	brain
22	chr7:98958200-98970000	Weak transcription	Fetal Heart	heart
23	chr7:98959400-98970400	Weak transcription	Psoas Muscle	Psoas
24	chr7:98959400-98971600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:98960800-98967200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:98960800-98968600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr7:98961200-98966800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:98961200-98967400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:98961200-98971600	Weak transcription	Small Intestine	intestine
30	chr7:98961800-98967400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:98962200-98971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:98962800-98967200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:98962800-98970000	Weak transcription	Fetal Kidney	kidney
34	chr7:98962800-98971400	Weak transcription	Primary B cells from cord blood	blood
35	chr7:98964200-98970000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:98964400-98966000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:98964400-98966400	Weak transcription	Hela-S3	cervix
38	chr7:98964400-98969000	Weak transcription	HepG2	liver
39	chr7:98964400-98970000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:98964400-98970200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr7:98964600-98967600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:98964600-98969200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:98964600-98970000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:98964600-98970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:98964600-98971600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr7:98964600-98971600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:98964800-98970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:98964800-98971400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:98964800-98971400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr7:98965000-98966200	Weak transcription	Rectal Mucosa Donor 31	rectum

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