Variant report

Variant	rs1568780
Chromosome Location	chr7:65203587-65203588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10950010	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950018	0.90[YRI][hapmap]
rs10950022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11760664	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534326	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2419266	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2419437	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28436091	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3734911	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3981841	0.88[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs4275112	0.89[CEU][hapmap]
rs4499980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717272	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4717273	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4718262	0.92[CEU][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs4718287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs55818599	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56115836	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460259	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6947487	0.92[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap]
rs6958860	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs6966573	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73136171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7778644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7786206	0.82[CHD][hapmap];0.84[GIH][hapmap]
rs7787713	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752165	chr7:64345822-65208605	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv517778	chr7:64462326-65326821	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv917231	chr7:64478253-65300317	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	esv2752166	chr7:64478386-65208605	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv1029796	chr7:64494934-65302696	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv533081	chr7:64499945-65208605	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
9	esv2758117	chr7:64551274-65208605	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv1029343	chr7:64566957-65208605	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv538894	chr7:64566957-65208605	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv607316	chr7:64582849-65208605	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	esv2764020	chr7:64594065-65351820	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv1018447	chr7:64609892-65308719	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv538897	chr7:64609892-65308719	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
18	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
19	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
20	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
21	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
22	esv2752170	chr7:64728078-65208605	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	esv2752171	chr7:64728078-65208605	Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	esv2752172	chr7:64728078-65208605	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
25	esv2752173	chr7:64830520-65208605	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
26	nsv888320	chr7:64956181-65208605	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
27	nsv428167	chr7:64980539-65208605	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
28	nsv1025207	chr7:65092426-65339879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
29	nsv1033400	chr7:65092426-65339879	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
30	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
31	nsv1020622	chr7:65161364-65339879	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1568780	ZNF273	cis	cerebellum	SCAN
rs1568780	RABGEF1	cis	cerebellum	SCAN
rs1568780	RP13-254B10.1	cis	Esophagus Mucosa	GTEx
rs1568780	GUSB	cis	parietal	SCAN
rs1568780	LOC168474	cis	cerebellum	SCAN
rs1568780	GUSB	cis	cerebellum	SCAN
rs1568780	ERV3	cis	parietal	SCAN
rs1568780	ZNF273	cis	parietal	SCAN
rs1568780	RP4-756H11.3	cis	Thyroid	GTEx
rs1568780	RP4-756H11.3	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65182600-65215200	Weak transcription	Brain Hippocampus Middle	brain
2	chr7:65187600-65205400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:65187600-65215000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr7:65188600-65215000	Weak transcription	HSMM	muscle
5	chr7:65189400-65203600	Weak transcription	Brain Substantia Nigra	brain
6	chr7:65189600-65210600	Weak transcription	A549	lung
7	chr7:65189600-65210800	Weak transcription	NHLF	lung
8	chr7:65190200-65205200	Weak transcription	Aorta	Aorta
9	chr7:65190800-65214600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:65191800-65215000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:65192200-65214200	Weak transcription	Liver	Liver
12	chr7:65192200-65214200	Weak transcription	Dnd41	blood
13	chr7:65194400-65214200	Weak transcription	GM12878-XiMat	blood
14	chr7:65195200-65215400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:65196000-65206400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:65196600-65215000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr7:65196800-65203600	Weak transcription	Ovary	ovary
18	chr7:65196800-65210800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr7:65196800-65214400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:65196800-65214600	Weak transcription	Primary B cells from cord blood	blood
21	chr7:65196800-65214600	Weak transcription	Brain Angular Gyrus	brain
22	chr7:65196800-65215400	Weak transcription	Small Intestine	intestine
23	chr7:65197000-65203600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:65197000-65203600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr7:65197000-65204200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:65197000-65204400	Weak transcription	Adipose Nuclei	Adipose
27	chr7:65197000-65204800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr7:65197000-65206200	Weak transcription	NHEK	skin
29	chr7:65197000-65209400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:65197000-65210000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:65197000-65210000	Weak transcription	Pancreas	Pancrea
32	chr7:65197000-65210200	Weak transcription	Fetal Lung	lung
33	chr7:65197000-65210600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:65197000-65210600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr7:65197000-65210800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:65197000-65210800	Weak transcription	Fetal Kidney	kidney
37	chr7:65197000-65211200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:65197000-65214400	Weak transcription	K562	blood
39	chr7:65197000-65214600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:65197000-65214600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:65197000-65214600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:65197000-65214600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:65197000-65214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:65197000-65215000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr7:65197000-65215000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr7:65197000-65215000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:65197000-65215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr7:65197000-65215000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:65197000-65215000	Weak transcription	Placenta	Placenta
50	chr7:65197000-65215200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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