Variant report

Variant	rs2286162
Chromosome Location	chr7:98955804-98955805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:98955344-98955818	K562	blood:	n/a	n/a
2	POLR2A	chr7:98955276-98955805	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:98954823-98956007	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98954568..98956787-chr7:98970778..98974586,3	K562	blood:
2	chr7:98953069..98956142-chr7:98957190..98959083,3	K562	blood:

Variant related genes	Relation type
ARPC1A	TF binding region
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10155966	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10225529	0.87[EUR][1000 genomes]
rs10232076	0.99[ASN][1000 genomes]
rs10236149	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10238965	0.92[CEU][hapmap]
rs10243678	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249167	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255399	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258757	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267346	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10270459	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270917	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10271049	0.92[CEU][hapmap]
rs10272998	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10274407	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279308	0.91[CEU][hapmap]
rs1043466	0.92[CEU][hapmap]
rs10953286	0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10953287	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11762273	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11771702	0.84[CEU][hapmap]
rs11976018	0.92[CEU][hapmap]
rs11978089	0.92[CEU][hapmap]
rs12112936	0.84[CEU][hapmap]
rs12113440	0.84[CEU][hapmap]
rs13240600	0.83[CEU][hapmap]
rs17161652	0.85[JPT][hapmap]
rs17161677	0.85[JPT][hapmap]
rs17161692	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17161695	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs1980307	0.92[CEU][hapmap]
rs2003499	0.91[CEU][hapmap]
rs2072181	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074652	0.85[JPT][hapmap]
rs2107922	0.86[EUR][1000 genomes]
rs2240384	0.92[CEU][hapmap]
rs2272168	0.92[CEU][hapmap]
rs2280600	0.92[CEU][hapmap]
rs2280601	0.92[CEU][hapmap]
rs2301889	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2404323	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28468623	0.98[ASN][1000 genomes]
rs28495024	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28820905	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3137	0.92[CEU][hapmap]
rs3801288	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843540	0.83[CEU][hapmap]
rs4729532	0.91[CEU][hapmap]
rs58660994	0.98[ASN][1000 genomes]
rs59725656	0.98[ASN][1000 genomes]
rs6943920	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948775	0.99[ASN][1000 genomes]
rs6953476	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6955490	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6962772	0.92[CEU][hapmap]
rs6972337	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975099	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73395547	0.98[ASN][1000 genomes]
rs73395557	0.98[ASN][1000 genomes]
rs73395580	0.99[ASN][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794705	0.92[CEU][hapmap]
rs883403	0.92[CEU][hapmap]
rs917154	0.91[CEU][hapmap]
rs9641253	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768020	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9918551	0.98[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
rs2286162	ARPC1B	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924400-98957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:98925200-98965200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:98927200-98966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:98927800-98960600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:98928400-98967200	Strong transcription	Fetal Thymus	thymus
7	chr7:98928600-98965200	Strong transcription	Dnd41	blood
8	chr7:98929000-98965600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:98929400-98965200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:98929600-98962800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr7:98929600-98965400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:98929800-98965000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr7:98930000-98962800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:98930000-98968200	Strong transcription	Fetal Intestine Small	intestine
15	chr7:98930200-98968400	Strong transcription	Fetal Stomach	stomach
16	chr7:98930600-98965200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:98930600-98965200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:98930600-98965200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:98930800-98960200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:98930800-98965200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:98930800-98965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:98930800-98965400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:98930800-98966800	Strong transcription	Adipose Nuclei	Adipose
24	chr7:98930800-98967000	Strong transcription	Fetal Muscle Leg	muscle
25	chr7:98930800-98967600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr7:98931000-98959600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:98931000-98960200	Strong transcription	Placenta	Placenta
28	chr7:98931000-98965000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:98932600-98966400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:98934400-98965200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr7:98935600-98971600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:98939600-98965400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr7:98939800-98965200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:98939800-98965200	Strong transcription	Fetal Intestine Large	intestine
35	chr7:98940000-98957200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:98940200-98965000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:98940600-98965000	Strong transcription	Primary T cells from cord blood	blood
38	chr7:98941200-98959800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr7:98941200-98963000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:98941600-98965200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:98943400-98957800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:98944200-98967200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr7:98944400-98959200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr7:98944400-98965200	Strong transcription	Thymus	Thymus
45	chr7:98944400-98965400	Strong transcription	Spleen	Spleen
46	chr7:98944600-98965200	Strong transcription	Lung	lung
47	chr7:98945600-98963200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:98945600-98963200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr7:98946400-98957200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:98946400-98967600	Strong transcription	Stomach Smooth Muscle	stomach

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