Variant report

Variant	rs654523
Chromosome Location	chr1:210413739-210413740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210407396..210411082-chr1:210412601..210414553,3	MCF-7	breast:
2	chr1:210412478..210415136-chr1:210418022..210419994,2	MCF-7	breast:
3	chr1:210413315..210414870-chr1:210546100..210547837,2	K562	blood:
4	chr1:210413315..210414870-chr1:210546100..210548763,3	K562	blood:
5	chr1:210411288..210415532-chr1:210545845..210548643,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082497	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11119444	0.85[ASN][1000 genomes]
rs12125619	0.94[CHD][hapmap]
rs12239420	0.94[ASN][1000 genomes]
rs1338298	1.00[YRI][hapmap]
rs1342135	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2473814	0.89[ASN][1000 genomes]
rs2487904	0.83[ASN][1000 genomes]
rs2494180	0.83[ASN][1000 genomes]
rs2494183	0.84[YRI][hapmap]
rs2494184	0.84[YRI][hapmap]
rs2494185	0.92[ASN][1000 genomes]
rs2494186	0.93[ASN][1000 genomes]
rs34463765	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4844981	0.90[ASN][1000 genomes]
rs624270	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs624706	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs656312	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs660611	0.94[ASN][1000 genomes]
rs674513	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs677520	0.93[ASN][1000 genomes]
rs685532	0.80[GIH][hapmap];0.80[JPT][hapmap]
rs845451	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9430037	0.93[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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs654523	SERTAD4-AS1	cis	Thyroid	GTEx
rs654523	NFASC	cis	parietal	SCAN
rs654523	TRAF5	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210407800-210424000	Weak transcription	Colonic Mucosa	Colon
2	chr1:210407800-210424000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:210407800-210424200	Weak transcription	Pancreas	Pancrea
4	chr1:210408000-210418200	Weak transcription	Esophagus	oesophagus
5	chr1:210408000-210424000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:210408200-210414800	Enhancers	Rectal Smooth Muscle	rectum
7	chr1:210408600-210413800	Enhancers	Fetal Heart	heart
8	chr1:210409600-210414000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:210409600-210414200	Enhancers	NHDF-Ad	bronchial
10	chr1:210409800-210414000	Enhancers	Fetal Lung	lung
11	chr1:210409800-210414200	Enhancers	NHLF	lung
12	chr1:210410800-210424000	Weak transcription	Lung	lung
13	chr1:210410800-210424200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:210411000-210414200	Enhancers	Fetal Stomach	stomach
15	chr1:210411000-210414800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:210411200-210413800	Enhancers	Colon Smooth Muscle	Colon
17	chr1:210411200-210413800	Enhancers	NH-A	brain
18	chr1:210411200-210423600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:210411400-210414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:210411400-210423800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:210411600-210413800	Weak transcription	Left Ventricle	heart
22	chr1:210411600-210414800	Enhancers	HSMM	muscle
23	chr1:210411600-210418000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:210411600-210418400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:210411800-210413800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:210411800-210414000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:210411800-210414200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:210411800-210422200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:210411800-210423600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:210411800-210423600	Weak transcription	Brain Anterior Caudate	brain
31	chr1:210411800-210423800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:210412000-210413800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:210412000-210413800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:210412000-210413800	Weak transcription	Brain Substantia Nigra	brain
35	chr1:210412000-210422800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:210412000-210423800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:210412600-210413800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:210412600-210413800	Enhancers	A549	lung
39	chr1:210412600-210414000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:210412800-210414000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:210412800-210414200	Genic enhancers	HMEC	breast
42	chr1:210412800-210414600	Enhancers	HSMMtube	muscle
43	chr1:210413000-210413800	Flanking Active TSS	Osteobl	bone
44	chr1:210413000-210414000	Enhancers	Brain Hippocampus Middle	brain
45	chr1:210413200-210413800	Enhancers	Brain Cingulate Gyrus	brain
46	chr1:210413200-210414000	Enhancers	Right Atrium	heart
47	chr1:210413200-210414000	Enhancers	Stomach Smooth Muscle	stomach
48	chr1:210413200-210414400	Enhancers	HUVEC	blood vessel
49	chr1:210413400-210413800	Weak transcription	Ovary	ovary
50	chr1:210413400-210414200	Genic enhancers	Fetal Muscle Leg	muscle

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