Variant report

Variant	rs4849178
Chromosome Location	chr2:113982608-113982609
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	chr2:113982408-113988487	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113982222..113985690-chr2:113985752..113988361,3	MCF-7	breast:
2	chr2:113978254..113980033-chr2:113981611..113983261,2	MCF-7	breast:
3	chr2:113976625..113978334-chr2:113981431..113983858,2	K562	blood:
4	chr2:113976337..113978334-chr2:113981431..113983858,3	K562	blood:

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

Extended variants
information (count: 24 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1015753	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1015754	0.88[CEU][hapmap]
rs1015755	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1049137	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1077855	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12472361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12998725	1.00[YRI][hapmap]
rs2166421	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289897	0.88[AMR][1000 genomes]
rs28522253	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2863242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28679654	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35222158	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35606997	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3738913	0.92[ASN][1000 genomes]
rs4849180	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849182	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849186	1.00[YRI][hapmap]
rs6736334	0.92[AMR][1000 genomes];0.82[EUR][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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4849178	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs4849178	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs4849178	PAX8	cis	parietal	SCAN
rs4849178	PAX8	cis	lymphoblastoid	seeQTL
rs4849178	LOC654433	cis	parietal	SCAN
rs4849178	AC016683.6	cis	Whole Blood	GTEx
rs4849178	AC016683.6	cis	Artery Tibial	GTEx
rs4849178	LOC654433	cis	cerebellum	SCAN
rs4849178	AC016683.6	cis	Esophagus Muscularis	GTEx
rs4849178	PAX8	cis	Adipose Subcutaneous	GTEx
rs4849178	AC016683.6	cis	lung	GTEx
rs4849178	PAX8	cis	multi-tissue	Pritchard
rs4849178	AC016683.6	cis	Muscle Skeletal	GTEx
rs4849178	AC016683.6	cis	Esophagus Mucosa	GTEx
rs4849178	PAX8	cis	Whole Blood	GTEx
rs4849178	PAX8	cis	lung	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113970800-113983000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:113972200-113982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:113975600-113983600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:113975800-113983000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:113975800-113983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:113976400-113982800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:113976600-113983200	Weak transcription	Fetal Lung	lung
8	chr2:113977400-113985600	Weak transcription	Gastric	stomach
9	chr2:113977600-113983000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:113977800-113983600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:113978000-113983000	Weak transcription	Osteobl	bone
12	chr2:113978000-113983200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:113978000-113983200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:113978000-113986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:113978000-113987600	Weak transcription	Esophagus	oesophagus
16	chr2:113978200-113983000	Weak transcription	Fetal Stomach	stomach
17	chr2:113978200-113983200	Weak transcription	Fetal Intestine Small	intestine
18	chr2:113978200-113987200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:113978200-113991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:113978400-113983000	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:113978400-113983600	Weak transcription	Lung	lung
22	chr2:113978400-113983600	Weak transcription	Pancreas	Pancrea
23	chr2:113978600-113983000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:113978600-113984600	Genic enhancers	Fetal Kidney	kidney
25	chr2:113978800-113986200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:113979600-113982800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:113980000-113982800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:113980000-113982800	Weak transcription	Stomach Mucosa	stomach
29	chr2:113980000-113983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:113980200-113983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:113980200-113991600	Weak transcription	Spleen	Spleen
32	chr2:113982000-113983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:113982400-113983200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:113982400-113984200	Enhancers	Fetal Intestine Large	intestine
35	chr2:113982600-113982800	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:113982600-113982800	Enhancers	A549	lung
37	chr2:113982600-113983800	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:113982600-113983800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:113982600-113984000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:113982600-113984000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:113982600-113984000	Enhancers	NH-A	brain
42	chr2:113982600-113984200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:113982600-113984200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:113982600-113984200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:113982600-113984200	Enhancers	Brain Anterior Caudate	brain
46	chr2:113982600-113984400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:113982600-113984400	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr2:113982600-113984600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:113982600-113984800	Enhancers	HepG2	liver
50	chr2:113982600-113987000	Enhancers	Cortex derived primary cultured neurospheres	brain

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