Variant report

Variant	rs6736334
Chromosome Location	chr2:113971599-113971600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113970718..113973548-chr2:113977522..113979126,2	MCF-7	breast:
2	chr2:113971527..113973415-chr2:113977067..113979032,2	K562	blood:
3	chr2:113968482..113971643-chr2:113991034..113994286,5	MCF-7	breast:
4	chr2:113970934..113973261-chr2:113995727..113997421,2	MCF-7	breast:
5	chr2:113923220..113926121-chr2:113970035..113971940,2	K562	blood:
6	chr2:113968914..113973967-chr2:113991743..113995400,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1015753	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1015754	0.81[AFR][1000 genomes]
rs1015755	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1049137	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1077855	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123169	0.80[AFR][1000 genomes]
rs12472361	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2166421	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2289897	0.80[AMR][1000 genomes]
rs28522253	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2863242	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28679654	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35222158	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35606997	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849178	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4849180	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4849182	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs931472	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6736334	PAX8	cis	lung	GTEx
rs6736334	AC016683.6	cis	Whole Blood	GTEx
rs6736334	AC016683.6	cis	Artery Tibial	GTEx
rs6736334	PAX8	cis	Whole Blood	GTEx
rs6736334	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs6736334	AC016683.6	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:113960800-113975000	Weak transcription	Liver	Liver
6	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
7	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:113964000-113972800	Enhancers	Fetal Kidney	kidney
9	chr2:113966200-113972000	Enhancers	Fetal Stomach	stomach
10	chr2:113967600-113975200	Weak transcription	Gastric	stomach
11	chr2:113968200-113973200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:113968200-113973200	Enhancers	HepG2	liver
13	chr2:113968400-113971800	Enhancers	Brain Germinal Matrix	brain
14	chr2:113968400-113972000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:113969000-113971600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:113969000-113971800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:113969400-113974800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:113969400-113975400	Weak transcription	Right Ventricle	heart
19	chr2:113969600-113971600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:113969600-113973000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:113969600-113973000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:113969600-113974800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:113969600-113974800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:113969800-113974600	Weak transcription	Brain Substantia Nigra	brain
25	chr2:113969800-113974800	Weak transcription	Fetal Thymus	thymus
26	chr2:113970000-113971800	Weak transcription	HMEC	breast
27	chr2:113970000-113972600	Enhancers	NHEK	skin
28	chr2:113970000-113973200	Enhancers	A549	lung
29	chr2:113970000-113974400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:113970000-113974400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:113970000-113974400	Weak transcription	HSMMtube	muscle
32	chr2:113970000-113975000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:113970000-113975000	Weak transcription	Osteobl	bone
34	chr2:113970000-113975400	Weak transcription	Stomach Mucosa	stomach
35	chr2:113970200-113971800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:113970200-113972000	Enhancers	Esophagus	oesophagus
37	chr2:113970200-113974600	Weak transcription	HSMM	muscle
38	chr2:113970400-113974600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:113970400-113974800	Weak transcription	Small Intestine	intestine
40	chr2:113970400-113975000	Weak transcription	Hela-S3	cervix
41	chr2:113970400-113975600	Weak transcription	NHLF	lung
42	chr2:113970600-113971600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:113970600-113973800	Weak transcription	Fetal Intestine Large	intestine
44	chr2:113970600-113973800	Weak transcription	Fetal Intestine Small	intestine
45	chr2:113970600-113973800	Weak transcription	Left Ventricle	heart
46	chr2:113970600-113974400	Weak transcription	NH-A	brain
47	chr2:113970600-113974600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr2:113970600-113974600	Weak transcription	Colonic Mucosa	Colon
49	chr2:113970600-113974600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:113970600-113974800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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