Variant report

Variant	rs10953287
Chromosome Location	chr7:98922422-98922423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:98922203-98924097	K562	blood:	n/a	n/a
2	POLR2A	chr7:98921519-98924152	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:98921734-98924171	HepG2	liver:	n/a	n/a
4	JUN	chr7:98922159-98924851	K562	blood:	n/a	chr7:98924136-98924143 chr7:98922377-98922386
5	POLR2A	chr7:98922221-98922480	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr7:98922207-98922607	K562	blood:	n/a	n/a
7	POLR2A	chr7:98922028-98923872	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr7:98922327-98923832	GM12892	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98912362..98913995-chr7:98921766..98923287,2	MCF-7	breast:
2	chr7:98922130..98924896-chr7:98987117..98989793,2	K562	blood:
3	chr7:98921655..98927239-chr7:98969297..98973851,7	MCF-7	breast:
4	chr7:98915217..98917210-chr7:98919923..98922724,2	K562	blood:
5	chr7:98921250..98923226-chr7:98924796..98927676,2	MCF-7	breast:
6	chr7:98921987..98924595-chr7:99004669..99006776,2	K562	blood:

No data

Variant related genes	Relation type
ARPC1A	TF binding region
ENSG00000130429	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10155966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10225529	0.87[EUR][1000 genomes]
rs10232076	0.98[ASN][1000 genomes]
rs10236149	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10243678	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249167	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255399	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258757	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267346	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10270459	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270917	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10272998	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274407	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762273	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161692	0.98[ASN][1000 genomes]
rs17161695	0.87[EUR][1000 genomes]
rs2072181	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2107922	0.86[EUR][1000 genomes]
rs2286162	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301889	0.99[ASN][1000 genomes]
rs2404323	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28468623	0.99[ASN][1000 genomes]
rs28495024	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28820905	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801288	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58660994	0.99[ASN][1000 genomes]
rs59725656	0.97[ASN][1000 genomes]
rs6943920	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948775	0.98[ASN][1000 genomes]
rs6953476	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955490	0.81[EUR][1000 genomes]
rs6972337	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975099	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395547	0.99[ASN][1000 genomes]
rs73395557	0.99[ASN][1000 genomes]
rs73395580	0.98[ASN][1000 genomes]
rs9641253	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9768020	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9918551	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10953287	ARPC1B	cis	Thyroid	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98908200-98922600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:98908400-98923000	Weak transcription	Aorta	Aorta
3	chr7:98910600-98922600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:98911000-98922600	Weak transcription	NHLF	lung
5	chr7:98911200-98922600	Weak transcription	Brain Substantia Nigra	brain
6	chr7:98911400-98922600	Weak transcription	A549	lung
7	chr7:98915000-98922600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:98918600-98922600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:98919400-98922600	Weak transcription	Stomach Mucosa	stomach
10	chr7:98920000-98922600	Weak transcription	Fetal Heart	heart
11	chr7:98920000-98922600	Weak transcription	HUVEC	blood vessel
12	chr7:98920400-98922800	Weak transcription	Left Ventricle	heart
13	chr7:98920600-98922600	Weak transcription	Fetal Stomach	stomach
14	chr7:98921800-98922600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:98921800-98922600	Enhancers	Brain Germinal Matrix	brain
16	chr7:98921800-98922600	Enhancers	Right Ventricle	heart
17	chr7:98921800-98922800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:98921800-98922800	Enhancers	Liver	Liver
19	chr7:98921800-98922800	Enhancers	Pancreas	Pancrea
20	chr7:98922000-98922600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:98922000-98922600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:98922200-98922600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:98922200-98922600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:98922200-98922600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr7:98922200-98922600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr7:98922200-98922800	Flanking Active TSS	HepG2	liver
27	chr7:98922200-98923200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:98922200-98924800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr7:98922400-98922600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:98922400-98922600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:98922400-98922600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:98922400-98922600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:98922400-98922600	Enhancers	Primary T cells from cord blood	blood
34	chr7:98922400-98922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr7:98922400-98922600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:98922400-98922600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr7:98922400-98922600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:98922400-98922600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:98922400-98922600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:98922400-98922600	Enhancers	Adipose Nuclei	Adipose
41	chr7:98922400-98922600	Enhancers	Brain Hippocampus Middle	brain
42	chr7:98922400-98922600	Enhancers	Duodenum Mucosa	Duodenum
43	chr7:98922400-98922600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr7:98922400-98922600	Active TSS	Fetal Brain Female	brain
45	chr7:98922400-98922600	Enhancers	Fetal Intestine Large	intestine
46	chr7:98922400-98922600	Enhancers	Fetal Muscle Trunk	muscle
47	chr7:98922400-98922600	Enhancers	Fetal Muscle Leg	muscle
48	chr7:98922400-98922600	Enhancers	Fetal Thymus	thymus
49	chr7:98922400-98922600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr7:98922400-98922600	Enhancers	Skeletal Muscle Male	skeletal muscle

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