Variant report

Variant	rs59844139
Chromosome Location	chr2:172731983-172731984
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172730405..172732690-chr2:172749588..172752325,2	K562	blood:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10930491	0.81[AMR][1000 genomes]
rs11690807	0.85[AMR][1000 genomes]
rs12997093	0.81[AMR][1000 genomes]
rs1607254	0.85[AMR][1000 genomes]
rs17581284	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271758	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292816	0.83[AMR][1000 genomes]
rs34242651	0.81[AMR][1000 genomes]
rs34531723	0.81[AMR][1000 genomes]
rs35854151	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770458	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62182403	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62184165	0.81[AMR][1000 genomes]
rs6723259	0.85[AMR][1000 genomes]
rs9789538	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59844139	AC068039.4	cis	Esophagus Muscularis	GTEx
rs59844139	AC068039.4	cis	Thyroid	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172690200-172750200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172691400-172738600	Weak transcription	Esophagus	oesophagus
3	chr2:172692200-172733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:172693400-172734800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:172693600-172734400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:172693600-172734600	Weak transcription	HSMM	muscle
7	chr2:172693800-172732600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:172693800-172734600	Weak transcription	Right Ventricle	heart
9	chr2:172694000-172732800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:172694000-172734600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:172694000-172734600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:172698600-172734600	Weak transcription	Adipose Nuclei	Adipose
13	chr2:172699000-172734600	Weak transcription	Brain Angular Gyrus	brain
14	chr2:172705400-172735200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:172709400-172734400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:172709600-172749600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:172709600-172749600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:172710800-172747800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:172711600-172740000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:172712200-172749200	Weak transcription	Hela-S3	cervix
21	chr2:172712400-172738200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:172715400-172732600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:172715400-172735200	Weak transcription	NHLF	lung
24	chr2:172716600-172736600	Weak transcription	Ovary	ovary
25	chr2:172721200-172734600	Weak transcription	Right Atrium	heart
26	chr2:172721200-172734600	Weak transcription	HSMMtube	muscle
27	chr2:172721200-172749600	Weak transcription	Thymus	Thymus
28	chr2:172721400-172732400	Weak transcription	HMEC	breast
29	chr2:172721400-172732600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:172721400-172734600	Weak transcription	Aorta	Aorta
31	chr2:172721400-172734600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:172721400-172734600	Weak transcription	Psoas Muscle	Psoas
33	chr2:172721600-172733200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:172721800-172732800	Weak transcription	Fetal Heart	heart
35	chr2:172723200-172733800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:172724000-172749600	Weak transcription	Small Intestine	intestine
37	chr2:172724600-172733600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:172724800-172749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:172725200-172734600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:172725200-172735000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:172725400-172732800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:172725400-172749800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:172725800-172732400	Weak transcription	Osteobl	bone
44	chr2:172725800-172732600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:172725800-172734400	Weak transcription	K562	blood
46	chr2:172725800-172749600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:172727800-172738600	Weak transcription	Dnd41	blood
48	chr2:172728000-172733800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:172728200-172734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:172730400-172732000	Strong transcription	Left Ventricle	heart

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