Variant report

Variant	rs7578249
Chromosome Location	chr2:114513386-114513387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:114512789..114515409-chr20:55840179..55841852,2	MCF-7	breast:
2	chr2:114512629..114516386-chr2:114645660..114650521,15	K562	blood:
3	chr2:114491572..114494215-chr2:114513189..114515373,3	K562	blood:
4	chr2:114512297..114513973-chr2:114517803..114519961,2	MCF-7	breast:
5	chr2:114513011..114515179-chr2:114599381..114601639,2	MCF-7	breast:
6	chr2:114510034..114517579-chr2:114643441..114655407,23	MCF-7	breast:
7	chr2:114512680..114516386-chr2:114646106..114650521,15	K562	blood:
8	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
9	chr2:114512943..114515625-chr2:114589095..114591354,2	MCF-7	breast:
10	chr2:114511724..114513896-chr2:114718190..114720983,2	K562	blood:
11	chr2:114489220..114494215-chr2:114513189..114517576,5	K562	blood:
12	chr2:114512708..114514375-chr2:114682269..114685341,3	MCF-7	breast:
13	chr2:114501133..114502988-chr2:114513074..114515544,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115084	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000228857	Chromatin interaction
ENSG00000115091	Chromatin interaction
ENSG00000270019	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10168234	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199704	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200355	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10205467	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206174	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11679707	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11682259	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695798	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11897553	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901060	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711784	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711786	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006627	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13029093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13034531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13397540	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13405475	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13416930	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1349157	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17048473	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305254	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2418915	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35432356	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35667749	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4849264	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849265	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849266	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4849269	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213422	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56376185	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58473055	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6542171	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6704673	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6739072	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741521	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67850681	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561176	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7586800	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7587218	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7590375	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7592689	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600550	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935644	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9798411	0.84[AMR][1000 genomes];0.84[EUR][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	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7578249	DDX11L2	cis	Whole Blood	GTEx
rs7578249	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs7578249	PS1TP4	Cis_1M	lymphoblastoid	RTeQTL
rs7578249	SLC35F5	cis	Skin Sun Exposed Lower leg	GTEx
rs7578249	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs7578249	RPL23AP7	cis	Whole Blood	GTEx
rs7578249	RPL23AP7	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114507000-114513400	Weak transcription	Spleen	Spleen
2	chr2:114508800-114513400	Weak transcription	Lung	lung
3	chr2:114509400-114513400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:114509400-114513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:114511200-114515000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:114511600-114515200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:114512000-114513400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:114512000-114513400	Flanking Active TSS	Dnd41	blood
9	chr2:114512000-114514600	Active TSS	HSMMtube	muscle
10	chr2:114512000-114514800	Active TSS	HMEC	breast
11	chr2:114512000-114515200	Active TSS	NHDF-Ad	bronchial
12	chr2:114512000-114515200	Active TSS	NHLF	lung
13	chr2:114512000-114515400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:114512200-114513400	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr2:114512200-114513600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr2:114512200-114513800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr2:114512200-114513800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:114512200-114513800	Active TSS	Right Atrium	heart
19	chr2:114512200-114514800	Active TSS	NHEK	skin
20	chr2:114512200-114515000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:114512200-114515000	Active TSS	GM12878-XiMat	blood
22	chr2:114512200-114515200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:114512200-114515200	Active TSS	HSMM	muscle
24	chr2:114512200-114515400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:114512400-114513600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:114512400-114513600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:114512400-114514600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:114512400-114514600	Active TSS	Stomach Smooth Muscle	stomach
29	chr2:114512400-114514800	Active TSS	Fetal Kidney	kidney
30	chr2:114512400-114514800	Active TSS	Osteobl	bone
31	chr2:114512400-114515200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:114512400-114515200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:114512400-114515200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:114512400-114515200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:114512400-114515200	Active TSS	Fetal Intestine Large	intestine
36	chr2:114512400-114515200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:114512400-114515200	Active TSS	NH-A	brain
38	chr2:114512400-114515400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:114512400-114515400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:114512400-114515400	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr2:114512400-114515400	Active TSS	A549	lung
42	chr2:114512600-114513400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:114512600-114513400	Flanking Active TSS	Liver	Liver
44	chr2:114512600-114513400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr2:114512600-114513600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr2:114512600-114514800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr2:114512600-114514800	Bivalent/Poised TSS	HepG2	liver
48	chr2:114512600-114515000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:114512600-114515000	Active TSS	Left Ventricle	heart
50	chr2:114512600-114515000	Active TSS	Ovary	ovary

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