Variant report

Variant	rs62253583
Chromosome Location	chr3:52928334-52928335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52925161..52929038-chr3:52929982..52933172,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248592	Chromatin interaction
ENSG00000213533	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10865977	0.81[ASN][1000 genomes]
rs11130331	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11922975	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12629687	0.85[ASN][1000 genomes]
rs12638968	0.80[EUR][1000 genomes]
rs2336664	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2336667	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2336668	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821873	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687562	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687679	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4687682	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687683	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687684	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687687	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56383738	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6795646	0.81[AMR][1000 genomes]
rs7626551	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9810807	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9836499	0.81[ASN][1000 genomes]
rs9850563	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9865248	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9866243	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9871175	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9880619	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9880978	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9985365	0.80[EUR][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	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62253583	ITIH4-AS1	cis	lung	GTEx
rs62253583	ITIH4-AS1	cis	Artery Tibial	GTEx
rs62253583	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
2	chr3:52908400-52930600	Weak transcription	A549	lung
3	chr3:52910000-52929400	Weak transcription	HMEC	breast
4	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:52916400-52930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:52919200-52930200	Weak transcription	Fetal Kidney	kidney
12	chr3:52920000-52929200	Weak transcription	Dnd41	blood
13	chr3:52920200-52929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:52920200-52929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:52920400-52930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52920400-52930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:52920400-52930600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:52921600-52930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52923800-52928800	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:52924000-52929400	Enhancers	Brain Hippocampus Middle	brain
21	chr3:52924000-52930000	Enhancers	Brain Substantia Nigra	brain
22	chr3:52924200-52930200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:52924400-52928400	Enhancers	Stomach Mucosa	stomach
24	chr3:52924600-52930200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:52924800-52929600	Genic enhancers	Thymus	Thymus
26	chr3:52925000-52928800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:52925200-52928400	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:52925200-52928400	Flanking Active TSS	GM12878-XiMat	blood
29	chr3:52925200-52928800	Enhancers	Adipose Nuclei	Adipose
30	chr3:52925200-52929600	Genic enhancers	Fetal Thymus	thymus
31	chr3:52925400-52928400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:52925400-52929800	Enhancers	Brain Anterior Caudate	brain
33	chr3:52925400-52929800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:52925400-52929800	Weak transcription	NHEK	skin
35	chr3:52925600-52928800	Weak transcription	Brain Germinal Matrix	brain
36	chr3:52925600-52930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:52925600-52930600	Weak transcription	Esophagus	oesophagus
38	chr3:52926000-52928600	Enhancers	Psoas Muscle	Psoas
39	chr3:52926000-52929200	Enhancers	Colon Smooth Muscle	Colon
40	chr3:52926000-52929800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:52926000-52930200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:52926200-52928600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:52926200-52930400	Weak transcription	Placenta	Placenta
44	chr3:52926400-52928800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:52926400-52930000	Weak transcription	Fetal Heart	heart
46	chr3:52926400-52930200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:52926400-52930200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:52926600-52929200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:52926600-52929400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:52926600-52929800	Enhancers	Brain Angular Gyrus	brain

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