Variant report

Variant	rs7355523
Chromosome Location	chr2:172744421-172744422
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172744007..172746435-chr2:172749737..172751670,2	MCF-7	breast:
2	chr2:172736226..172738889-chr2:172742380..172745045,2	K562	blood:
3	chr2:172737251..172741632-chr2:172744127..172746151,4	K562	blood:
4	chr2:172720314..172722919-chr2:172744324..172746947,2	K562	blood:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10166005	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10167419	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10174525	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10184866	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10194102	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10200608	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10201419	0.84[EUR][1000 genomes]
rs10204502	0.86[AMR][1000 genomes]
rs10204622	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10206062	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10207085	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10432423	0.87[EUR][1000 genomes]
rs10497374	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10803863	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1113389	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11678984	0.83[EUR][1000 genomes]
rs11757	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11886820	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11897196	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11904009	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12053003	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12185567	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12692970	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12692973	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12692974	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12692978	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13017585	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13018768	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13022113	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13419987	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13429113	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13429409	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1474074	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1554166	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1973706	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2292815	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2357061	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2674484	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2678155	0.80[AMR][1000 genomes]
rs312916	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs312918	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs312919	0.86[AMR][1000 genomes]
rs312921	0.80[AMR][1000 genomes]
rs312924	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs312925	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34358700	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34542126	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35379278	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35391289	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35549875	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35854280	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36057702	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3770445	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3770451	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3770452	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3795999	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4667693	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4667694	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4668412	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4668414	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433311	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6433314	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66835971	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6705200	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6709156	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6710698	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67204065	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6721680	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6722757	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6724337	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6725388	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738445	0.87[EUR][1000 genomes]
rs6745143	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6754817	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6757773	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6758704	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6759575	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71013062	0.82[EUR][1000 genomes]
rs7355594	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7562356	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7572215	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7573003	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7586207	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7597387	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7604918	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7608403	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs908670	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs908671	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs973889	0.91[AMR][1000 genomes];0.86[EUR][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7355523	AC068039.4	cis	Thyroid	GTEx
rs7355523	AC068039.4	cis	Nerve Tibial	GTEx
rs7355523	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs7355523	AC068039.4	cis	lung	GTEx
rs7355523	AC068039.4	cis	Muscle Skeletal	GTEx
rs7355523	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs7355523	AC068039.4	cis	Esophagus Mucosa	GTEx
rs7355523	AC068039.4	cis	Esophagus Muscularis	GTEx
rs7355523	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs7355523	AC068039.4	cis	Heart Left Ventricle	GTEx
rs7355523	AC068039.4	cis	Stomach	GTEx
rs7355523	AC068039.4	cis	Whole Blood	GTEx

Chromatin state (count:86 , 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	chr2:172709600-172749600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:172709600-172749600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:172710800-172747800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:172712200-172749200	Weak transcription	Hela-S3	cervix
6	chr2:172721200-172749600	Weak transcription	Thymus	Thymus
7	chr2:172724000-172749600	Weak transcription	Small Intestine	intestine
8	chr2:172724800-172749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:172725400-172749800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:172725800-172749600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:172731400-172746400	Weak transcription	Fetal Lung	lung
12	chr2:172731600-172749600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:172731800-172746400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:172732000-172746000	Weak transcription	Fetal Brain Female	brain
15	chr2:172732000-172746400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:172732000-172746400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:172732000-172746600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:172732000-172748800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:172732000-172749400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:172732000-172749400	Weak transcription	A549	lung
21	chr2:172732000-172749600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:172732000-172749800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:172732000-172749800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr2:172732000-172750000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:172732200-172746400	Weak transcription	Primary B cells from cord blood	blood
26	chr2:172732200-172749600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:172732400-172749600	Weak transcription	Fetal Kidney	kidney
28	chr2:172732400-172749800	Weak transcription	Fetal Thymus	thymus
29	chr2:172732600-172747000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:172733000-172746400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:172733000-172749200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:172733000-172749400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:172735200-172749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:172735400-172746600	Weak transcription	HSMM	muscle
35	chr2:172735400-172748200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:172735400-172748400	Weak transcription	Brain Anterior Caudate	brain
37	chr2:172735400-172749400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:172735400-172749400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:172735400-172749400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:172735400-172749600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:172735400-172749600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:172735400-172749600	Weak transcription	NHDF-Ad	bronchial
43	chr2:172735400-172749600	Weak transcription	NHEK	skin
44	chr2:172735600-172746400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:172735600-172749600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:172735600-172749600	Weak transcription	Adipose Nuclei	Adipose
47	chr2:172735600-172749600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:172735600-172749600	Weak transcription	Brain Substantia Nigra	brain
49	chr2:172735600-172749600	Weak transcription	HMEC	breast
50	chr2:172735600-172749600	Weak transcription	NHLF	lung

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