Variant report

Variant	rs160640
Chromosome Location	chr7:65579292-65579293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:65578560-65580741	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:65579201-65579299	GM12878	blood:	n/a	n/a
3	CEBPB	chr7:65578947-65579297	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:46130134..46132159-chr7:65578645..65581188,2	MCF-7	breast:
2	chr7:65550364..65554176-chr7:65578691..65580881,4	K562	blood:
3	chr7:65550364..65553168-chr7:65578691..65580268,2	K562	blood:
4	chr7:65540799..65542994-chr7:65578683..65581272,2	MCF-7	breast:
5	chr7:65538951..65542131-chr7:65578976..65581332,4	MCF-7	breast:
6	chr7:65578700..65580373-chr7:65590797..65592694,2	MCF-7	breast:

No data

Variant related genes	Relation type
CRCP	TF binding region
ENSG00000126522	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000249319	Chromatin interaction
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10950025	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10950028	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11760805	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12666485	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12673308	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs160641	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2244226	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2451953	0.86[EUR][1000 genomes]
rs2460427	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2465121	0.81[EUR][1000 genomes]
rs313818	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs313823	0.87[EUR][1000 genomes]
rs316305	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs316306	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs316316	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs316320	0.83[EUR][1000 genomes]
rs316324	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs316328	0.88[EUR][1000 genomes]
rs4441996	0.88[EUR][1000 genomes]
rs67302640	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67688847	0.81[EUR][1000 genomes]
rs6960870	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73136346	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73378304	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7787063	0.81[AFR][1000 genomes];0.81[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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs160640	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs160640	GTF2IRD1P1	cis	Thyroid	GTEx
rs160640	GS1-124K5.4	cis	Whole Blood	GTEx
rs160640	GS1-124K5.11	cis	Thyroid	GTEx
rs160640	RP4-756H11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65565200-65579800	Weak transcription	Spleen	Spleen
2	chr7:65565800-65579400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:65573000-65579400	Weak transcription	HSMMtube	muscle
4	chr7:65574200-65579400	Weak transcription	Fetal Brain Female	brain
5	chr7:65574600-65579400	Weak transcription	Left Ventricle	heart
6	chr7:65575400-65579400	Weak transcription	Stomach Mucosa	stomach
7	chr7:65576400-65579400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:65576600-65579400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:65576600-65579400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:65576800-65579400	Weak transcription	NH-A	brain
11	chr7:65578000-65579400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr7:65578600-65579400	Enhancers	NHDF-Ad	bronchial
13	chr7:65578800-65579400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:65578800-65579400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:65578800-65579400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr7:65578800-65579400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:65578800-65579400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:65578800-65579400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr7:65578800-65580600	Active TSS	Hela-S3	cervix
20	chr7:65578800-65580800	Active TSS	GM12878-XiMat	blood
21	chr7:65578800-65581200	Active TSS	A549	lung
22	chr7:65579000-65579400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:65579000-65579400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:65579000-65579400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr7:65579000-65579400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:65579000-65579400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr7:65579000-65579400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr7:65579000-65579400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:65579000-65579400	Enhancers	Brain Substantia Nigra	brain
30	chr7:65579000-65579400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr7:65579000-65579400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr7:65579000-65579400	Enhancers	Fetal Brain Male	brain
33	chr7:65579000-65579400	Enhancers	Fetal Intestine Large	intestine
34	chr7:65579000-65579400	Enhancers	Fetal Muscle Trunk	muscle
35	chr7:65579000-65579400	Enhancers	Fetal Thymus	thymus
36	chr7:65579000-65579400	Enhancers	Lung	lung
37	chr7:65579000-65579400	Enhancers	HMEC	breast
38	chr7:65579000-65579400	Enhancers	HUVEC	blood vessel
39	chr7:65579000-65579400	Enhancers	Osteobl	bone
40	chr7:65579000-65579600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr7:65579000-65579600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:65579000-65579800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:65579000-65579800	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr7:65579000-65580000	Active TSS	Adipose Nuclei	Adipose
45	chr7:65579000-65580400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:65579000-65580400	Active TSS	Colon Smooth Muscle	Colon
47	chr7:65579000-65580400	Active TSS	Rectal Smooth Muscle	rectum
48	chr7:65579000-65580400	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr7:65579000-65580600	Active TSS	Brain Angular Gyrus	brain
50	chr7:65579000-65580600	Active TSS	Duodenum Mucosa	Duodenum

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