Variant report

Variant	rs6725388
Chromosome Location	chr2:172730015-172730016
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172729575..172731751-chr2:172948719..172951234,2	K562	blood:
2	chr2:172729602..172731733-chr2:172737376..172738895,2	K562	blood:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10165126	0.80[CEU][hapmap]
rs10166005	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10167419	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10174055	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10174525	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10184866	0.84[AMR][1000 genomes]
rs10194102	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10200608	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10202823	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs10204622	0.84[AMR][1000 genomes]
rs10206062	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10207085	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10497374	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10803863	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10930502	0.80[CEU][hapmap]
rs1113389	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11678984	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11692132	0.85[YRI][hapmap]
rs11757	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11897196	0.84[AMR][1000 genomes]
rs11904009	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12185567	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12692970	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12692973	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12692974	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12692978	0.84[CEU][hapmap];0.93[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017585	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13018768	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13030911	0.84[AMR][1000 genomes]
rs13419987	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13429113	0.80[AMR][1000 genomes]
rs13429409	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1474074	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1554166	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1973706	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292815	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2674484	0.84[AMR][1000 genomes]
rs312916	0.84[AMR][1000 genomes]
rs312918	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs312924	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs312925	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs34358700	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35379278	0.81[ASN][1000 genomes]
rs35391289	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36057702	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3770445	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770451	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770452	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795999	0.81[AMR][1000 genomes]
rs4667693	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4667694	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4668412	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4668414	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433311	0.81[AMR][1000 genomes]
rs6433314	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433319	0.92[CEU][hapmap]
rs66835971	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6705200	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6709156	0.84[AMR][1000 genomes]
rs6710698	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs6715929	0.88[CEU][hapmap]
rs67204065	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721680	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6722757	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6724337	0.88[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727017	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes]
rs6731562	0.92[CEU][hapmap]
rs6738445	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs6745143	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6750058	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs6752812	0.83[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs6754817	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757773	0.88[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs6758704	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759575	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7355523	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7355594	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7562356	0.84[AMR][1000 genomes]
rs7563971	0.80[AMR][1000 genomes]
rs7564089	0.81[AMR][1000 genomes]
rs7572215	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7573003	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7586207	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597387	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs7604918	0.84[AMR][1000 genomes]
rs7608403	0.88[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs908670	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs908671	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs973889	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6725388	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6725388	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6725388	AC068039.4	cis	Nerve Tibial	GTEx
rs6725388	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6725388	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6725388	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6725388	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6725388	AC068039.4	cis	lung	GTEx
rs6725388	AC068039.4	cis	Stomach	GTEx
rs6725388	AC068039.4	cis	Muscle Skeletal	GTEx
rs6725388	SLC25A12	cis	multi-tissue	Pritchard
rs6725388	AC068039.4	cis	Thyroid	GTEx
rs6725388	AC068039.4	cis	Whole Blood	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	chr2:172699600-172731400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:172704800-172731000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:172705200-172731400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:172705400-172735200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:172709400-172734400	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:172709600-172749600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:172709600-172749600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:172709800-172731400	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:172710800-172747800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:172711400-172731000	Weak transcription	GM12878-XiMat	blood
24	chr2:172711600-172740000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:172712000-172731200	Weak transcription	Primary B cells from cord blood	blood
26	chr2:172712200-172731000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:172712200-172749200	Weak transcription	Hela-S3	cervix
28	chr2:172712400-172731400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:172712400-172738200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:172715400-172731200	Weak transcription	Fetal Lung	lung
31	chr2:172715400-172732600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:172715400-172735200	Weak transcription	NHLF	lung
33	chr2:172715600-172731200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:172716600-172736600	Weak transcription	Ovary	ovary
35	chr2:172719600-172731200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:172721200-172731200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:172721200-172734600	Weak transcription	Right Atrium	heart
38	chr2:172721200-172734600	Weak transcription	HSMMtube	muscle
39	chr2:172721200-172749600	Weak transcription	Thymus	Thymus
40	chr2:172721400-172731200	Weak transcription	Primary T cells from cord blood	blood
41	chr2:172721400-172731200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:172721400-172731400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:172721400-172731600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:172721400-172732400	Weak transcription	HMEC	breast
45	chr2:172721400-172732600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:172721400-172734600	Weak transcription	Aorta	Aorta
47	chr2:172721400-172734600	Weak transcription	Brain Anterior Caudate	brain
48	chr2:172721400-172734600	Weak transcription	Psoas Muscle	Psoas
49	chr2:172721600-172733200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:172721800-172732800	Weak transcription	Fetal Heart	heart

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