Variant report

Variant	rs2404323
Chromosome Location	chr7:98985396-98985397
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	chr7:98984209-98985606	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:98985266-98986294	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:98985395-98985483	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98960796..98963310-chr7:98983560..98985753,2	MCF-7	breast:
2	chr7:98981776..98988825-chr7:99001775..99008244,9	K562	blood:

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000106245	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10155966	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10236149	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10243678	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10249167	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255399	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10258757	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10267346	0.86[AMR][1000 genomes]
rs10270459	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10270917	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10272998	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10274407	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10279308	0.82[EUR][1000 genomes]
rs10953287	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11762273	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11973460	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11978089	0.82[EUR][1000 genomes]
rs17161698	0.83[ASN][1000 genomes]
rs2003499	0.80[EUR][1000 genomes]
rs2057905	0.83[ASN][1000 genomes]
rs2057906	0.84[ASN][1000 genomes]
rs2072181	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107922	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286162	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2404322	0.85[ASN][1000 genomes]
rs28495024	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28820905	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3801288	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6943920	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6953476	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6972337	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6975099	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9641253	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9768020	0.86[AMR][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
rs2404323	ARPC1B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
3	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
5	chr7:98978000-98987000	Weak transcription	Small Intestine	intestine
6	chr7:98978200-98989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:98978800-98989000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:98979000-98989600	Weak transcription	Stomach Mucosa	stomach
9	chr7:98979200-98987000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:98979200-98987000	Weak transcription	HSMM	muscle
11	chr7:98979200-98989600	Weak transcription	Brain Substantia Nigra	brain
12	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:98979600-98989800	Weak transcription	Fetal Heart	heart
14	chr7:98979600-98990200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:98979600-98990200	Weak transcription	Right Atrium	heart
16	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:98980600-98989600	Strong transcription	NHEK	skin
18	chr7:98980800-98990000	Strong transcription	NHLF	lung
19	chr7:98980800-99000600	Strong transcription	Dnd41	blood
20	chr7:98981000-98988400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:98981000-98993000	Strong transcription	A549	lung
22	chr7:98981200-98989800	Strong transcription	Fetal Intestine Small	intestine
23	chr7:98981200-98989800	Strong transcription	Thymus	Thymus
24	chr7:98981200-98990000	Strong transcription	K562	blood
25	chr7:98981400-98989800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr7:98981400-98989800	Strong transcription	Fetal Stomach	stomach
27	chr7:98981600-98989800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:98981800-98986800	Weak transcription	Fetal Brain Female	brain
29	chr7:98981800-98988800	Strong transcription	GM12878-XiMat	blood
30	chr7:98981800-98989800	Weak transcription	Fetal Brain Male	brain
31	chr7:98982400-98987200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:98982400-98987400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:98982400-98989600	Strong transcription	Spleen	Spleen
34	chr7:98982400-98989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:98982800-98989000	Strong transcription	Fetal Thymus	thymus
36	chr7:98983000-98988600	Strong transcription	Gastric	stomach
37	chr7:98983000-98989400	Strong transcription	Fetal Muscle Leg	muscle
38	chr7:98983000-98989600	Strong transcription	HMEC	breast
39	chr7:98983000-98989600	Strong transcription	HUVEC	blood vessel
40	chr7:98983000-98989800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:98983200-98989000	Strong transcription	Pancreas	Pancrea
42	chr7:98983200-98989000	Strong transcription	Right Ventricle	heart
43	chr7:98983200-98989200	Strong transcription	Colonic Mucosa	Colon
44	chr7:98983200-98989400	Strong transcription	Fetal Intestine Large	intestine
45	chr7:98983200-98989800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr7:98983200-98989800	Strong transcription	Lung	lung
47	chr7:98983200-98990000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:98983200-98990000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:98983200-98990000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:98983400-98985800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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