Variant report

Variant	rs4518552
Chromosome Location	chr7:66020829-66020830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:20255501..20256451-chr7:66020783..66021283,3	K562	blood:
2	chr7:65590686..65593391-chr7:66020104..66022935,2	K562	blood:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction
ENSG00000040608	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10081172	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10226294	0.82[EUR][1000 genomes]
rs10228381	0.83[EUR][1000 genomes]
rs10236665	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10237244	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10239200	0.81[EUR][1000 genomes]
rs10244602	0.82[EUR][1000 genomes]
rs10247852	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10252133	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10255813	0.82[EUR][1000 genomes]
rs10257393	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10262184	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10264619	0.86[EUR][1000 genomes]
rs10267834	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10273320	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10275413	0.87[EUR][1000 genomes]
rs10278343	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10278763	0.83[EUR][1000 genomes]
rs10280431	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10280717	0.81[EUR][1000 genomes]
rs10281734	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10282522	0.81[EUR][1000 genomes]
rs10479728	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12234826	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12334214	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13437901	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16868546	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17138208	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1895134	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2420598	0.84[EUR][1000 genomes]
rs28368585	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28455065	0.89[EUR][1000 genomes]
rs28474923	0.82[EUR][1000 genomes]
rs28526115	0.83[EUR][1000 genomes]
rs28606020	0.87[EUR][1000 genomes]
rs28615327	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28657758	0.83[EUR][1000 genomes]
rs3757419	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3823607	0.81[EUR][1000 genomes]
rs4587218	0.88[EUR][1000 genomes]
rs58123804	0.86[EUR][1000 genomes]
rs58973756	0.88[EUR][1000 genomes]
rs61093354	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6949083	0.84[EUR][1000 genomes]
rs6974601	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73133809	0.81[EUR][1000 genomes]
rs73133816	0.82[EUR][1000 genomes]
rs73133851	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73139941	0.81[EUR][1000 genomes]
rs73148698	0.81[EUR][1000 genomes]
rs73152708	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73152719	0.88[EUR][1000 genomes]
rs73152725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv3447484	chr7:65909457-66033145	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv888327	chr7:65938980-66029429	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4518552	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs4518552	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs4518552	GS1-124K5.12	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65999800-66022400	Strong transcription	Fetal Stomach	stomach
2	chr7:66001400-66022400	Weak transcription	Stomach Mucosa	stomach
3	chr7:66003800-66022200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr7:66003800-66022800	Strong transcription	Fetal Intestine Small	intestine
5	chr7:66004400-66052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:66004800-66037200	Weak transcription	Psoas Muscle	Psoas
7	chr7:66005200-66022400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr7:66006000-66022200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:66006200-66021000	Strong transcription	Fetal Intestine Large	intestine
10	chr7:66006200-66022200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:66006200-66022400	Strong transcription	Lung	lung
12	chr7:66006200-66022600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:66006200-66024400	Strong transcription	Fetal Muscle Leg	muscle
14	chr7:66006200-66024400	Strong transcription	Thymus	Thymus
15	chr7:66006400-66022800	Strong transcription	Brain Germinal Matrix	brain
16	chr7:66006600-66022800	Weak transcription	Fetal Brain Male	brain
17	chr7:66007600-66021000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:66008200-66022000	Weak transcription	Right Atrium	heart
19	chr7:66008200-66022200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:66008400-66022600	Weak transcription	Fetal Heart	heart
21	chr7:66008600-66056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr7:66008800-66022400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:66008800-66022400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr7:66008800-66022600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:66009000-66022800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:66009000-66023000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:66009000-66031400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:66009200-66023600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:66009200-66029400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:66011000-66037000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:66011600-66045000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:66012400-66024600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:66012600-66021000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:66012600-66022600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:66012600-66022600	Strong transcription	Liver	Liver
36	chr7:66012600-66024200	Strong transcription	Dnd41	blood
37	chr7:66013000-66031800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr7:66013200-66022400	Strong transcription	Ovary	ovary
39	chr7:66013200-66022600	Strong transcription	Placenta	Placenta
40	chr7:66013200-66022600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr7:66013600-66022200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:66014200-66022000	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:66014200-66022400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr7:66014200-66022600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:66014400-66021200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:66014400-66022600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr7:66014400-66024400	Strong transcription	Fetal Brain Female	brain
48	chr7:66014600-66022400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:66014800-66021600	Weak transcription	A549	lung
50	chr7:66014800-66022400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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