Variant report

Variant	rs56865224
Chromosome Location	chr2:113980736-113980737
allele	C/T
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	chr2:113979575-113981338	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113978488..113981632-chr2:113983864..113986982,3	K562	blood:
2	chr2:113980625..113982276-chr2:113996414..113999389,2	K562	blood:
3	chr2:113965870..113969424-chr2:113978380..113981725,3	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000258395	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10193733	0.81[AFR][1000 genomes]
rs2241975	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748915	0.80[AMR][1000 genomes]
rs3762498	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56865224	AC016683.6	cis	Whole Blood	GTEx
rs56865224	AC016683.6	cis	Nerve Tibial	GTEx
rs56865224	LOC654433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:113970600-113982600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:113970800-113983000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:113972200-113982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:113975600-113983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:113975800-113982600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:113975800-113983000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:113975800-113983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:113976400-113982800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:113976600-113983200	Weak transcription	Fetal Lung	lung
11	chr2:113977400-113985600	Weak transcription	Gastric	stomach
12	chr2:113977600-113982600	Weak transcription	NH-A	brain
13	chr2:113977600-113983000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:113977800-113982600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:113977800-113982600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:113977800-113983600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:113978000-113982600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:113978000-113982600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:113978000-113983000	Weak transcription	Osteobl	bone
20	chr2:113978000-113983200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:113978000-113983200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:113978000-113986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:113978000-113987600	Weak transcription	Esophagus	oesophagus
24	chr2:113978200-113983000	Weak transcription	Fetal Stomach	stomach
25	chr2:113978200-113983200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:113978200-113987200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr2:113978200-113991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:113978400-113981200	Enhancers	HepG2	liver
29	chr2:113978400-113983000	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:113978400-113983600	Weak transcription	Lung	lung
31	chr2:113978400-113983600	Weak transcription	Pancreas	Pancrea
32	chr2:113978600-113980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:113978600-113983000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:113978600-113984600	Genic enhancers	Fetal Kidney	kidney
35	chr2:113978800-113982600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:113978800-113986200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:113979000-113982600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:113979000-113982600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:113979400-113981000	Weak transcription	Fetal Intestine Large	intestine
40	chr2:113979600-113982800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:113980000-113982400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:113980000-113982600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:113980000-113982800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:113980000-113982800	Weak transcription	Stomach Mucosa	stomach
45	chr2:113980000-113983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:113980200-113982600	Weak transcription	A549	lung
47	chr2:113980200-113983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:113980200-113991600	Weak transcription	Spleen	Spleen

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