Variant report

Variant	rs4717322
Chromosome Location	chr7:66278207-66278208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10950054	0.81[ASN][1000 genomes]
rs10950055	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs11766583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12666079	0.92[AFR][1000 genomes]
rs12668022	0.87[ASN][1000 genomes]
rs1638728	1.00[YRI][hapmap]
rs1638735	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs17747939	0.89[ASN][1000 genomes]
rs17748121	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs1796212	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796218	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1796219	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1796226	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1796227	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1922722	0.81[ASN][1000 genomes]
rs2533284	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs2707851	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2901267	0.95[ASN][1000 genomes]
rs35244862	0.89[ASN][1000 genomes]
rs3735155	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs3800815	0.98[ASN][1000 genomes]
rs4718385	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4718410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718433	0.85[CHD][hapmap]
rs6944703	1.00[ASW][hapmap]
rs6960230	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6966953	0.92[AFR][1000 genomes]
rs6970767	0.95[ASN][1000 genomes]
rs6974046	1.00[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6979167	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73139927	0.95[ASN][1000 genomes]
rs73139974	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73377594	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv981513	chr7:66276464-66291614	Weak transcription Enhancers Strong transcription Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4717322	GTF2IRD1P1	cis	Thyroid	GTEx
rs4717322	GUSB	cis	parietal	SCAN
rs4717322	GUSB	cis	cerebellum	SCAN
rs4717322	CRCP	cis	parietal	SCAN
rs4717322	CRCP	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr7:66245600-66279200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:66245600-66279400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:66246200-66279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:66249400-66278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:66250000-66279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:66250000-66279200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:66250200-66278600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr7:66254000-66278400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:66254200-66278600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:66254600-66278600	Strong transcription	HSMM	muscle
13	chr7:66255600-66279800	Weak transcription	Right Atrium	heart
14	chr7:66256200-66278600	Strong transcription	Adipose Nuclei	Adipose
15	chr7:66256600-66278400	Strong transcription	Fetal Muscle Leg	muscle
16	chr7:66256600-66278600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:66256600-66279000	Strong transcription	Fetal Stomach	stomach
18	chr7:66257200-66278400	Strong transcription	Thymus	Thymus
19	chr7:66257600-66278600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:66259800-66278600	Strong transcription	HSMMtube	muscle
21	chr7:66259800-66278800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:66260000-66278600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:66260000-66278800	Strong transcription	Fetal Intestine Small	intestine
24	chr7:66261000-66281400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:66268200-66278400	Strong transcription	NHDF-Ad	bronchial
26	chr7:66269200-66278400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:66270200-66278600	Strong transcription	NHLF	lung
28	chr7:66274400-66278600	Weak transcription	Aorta	Aorta
29	chr7:66274600-66278600	Weak transcription	Hela-S3	cervix
30	chr7:66274600-66279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:66275200-66278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:66275600-66280600	Weak transcription	Brain Anterior Caudate	brain
33	chr7:66275600-66281200	Weak transcription	Right Ventricle	heart
34	chr7:66275800-66278600	Weak transcription	Lung	lung
35	chr7:66275800-66280600	Weak transcription	Spleen	Spleen
36	chr7:66276000-66278600	Weak transcription	Psoas Muscle	Psoas
37	chr7:66276000-66278800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:66276000-66280400	Weak transcription	Pancreas	Pancrea
39	chr7:66276000-66282200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr7:66276000-66282800	Weak transcription	Brain Germinal Matrix	brain
41	chr7:66276200-66278400	Weak transcription	K562	blood
42	chr7:66276200-66279800	Weak transcription	Brain Substantia Nigra	brain
43	chr7:66276200-66279800	Weak transcription	Colon Smooth Muscle	Colon
44	chr7:66276200-66279800	Weak transcription	A549	lung
45	chr7:66276200-66282000	Weak transcription	GM12878-XiMat	blood
46	chr7:66276200-66282200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:66276400-66279800	Weak transcription	Brain Angular Gyrus	brain
48	chr7:66276400-66280600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr7:66276400-66281000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:66276600-66278400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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