Variant report

Variant	rs4717328
Chromosome Location	chr7:66352665-66352666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCTD7-2	chr7:66352258-66355627	NONHSAT121240

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10235423	0.80[YRI][hapmap]
rs10267335	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10281796	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12530806	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12536410	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698546	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12698547	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13220977	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13227468	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13231140	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13241598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28441684	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28648401	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2901311	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34577323	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800817	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4717331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718412	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718422	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718430	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68168107	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	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
3	nsv981514	chr7:66310139-66366240	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv967329	chr7:66349389-66353665	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4717328	GUSB	cis	parietal	SCAN
rs4717328	RP4-756H11.3	cis	lung	GTEx
rs4717328	GUSB	cis	cerebellum	SCAN
rs4717328	CRCP	cis	cerebellum	SCAN
rs4717328	CRCP	cis	parietal	SCAN
rs4717328	RP4-756H11.3	cis	Thyroid	GTEx
rs4717328	RP4-756H11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66358400	Weak transcription	Brain Anterior Caudate	brain
2	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
5	chr7:66317200-66364400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:66319400-66364800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:66321200-66367800	Weak transcription	Aorta	Aorta
8	chr7:66322400-66364200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:66324400-66363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:66325200-66360200	Weak transcription	Psoas Muscle	Psoas
11	chr7:66325200-66366400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:66325400-66366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:66325400-66369400	Weak transcription	Fetal Brain Female	brain
14	chr7:66325600-66359000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:66325600-66363600	Weak transcription	Primary B cells from cord blood	blood
16	chr7:66325600-66363600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:66325600-66373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr7:66325800-66352800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:66325800-66359600	Weak transcription	Spleen	Spleen
20	chr7:66325800-66363400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:66325800-66363400	Weak transcription	Brain Substantia Nigra	brain
22	chr7:66325800-66365800	Weak transcription	Esophagus	oesophagus
23	chr7:66325800-66366400	Weak transcription	Right Ventricle	heart
24	chr7:66325800-66367000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:66325800-66367600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr7:66326000-66362000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:66326000-66363600	Weak transcription	Gastric	stomach
28	chr7:66326400-66358200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr7:66326400-66362600	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:66326400-66363000	Weak transcription	Lung	lung
31	chr7:66326400-66368200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:66326400-66371800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr7:66326600-66363000	Weak transcription	Fetal Stomach	stomach
34	chr7:66328200-66367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:66329600-66362000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:66329800-66372000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr7:66330400-66366000	Weak transcription	Fetal Thymus	thymus
38	chr7:66331200-66353800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:66331800-66378400	Weak transcription	A549	lung
40	chr7:66333000-66371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:66333400-66353800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr7:66333800-66364000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr7:66333800-66371800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:66334200-66367600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:66335000-66361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr7:66335000-66363800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:66335400-66371400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr7:66335600-66361400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:66335600-66363800	Weak transcription	Adipose Nuclei	Adipose
50	chr7:66336200-66364600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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