Variant report

Variant	rs11983033
Chromosome Location	chr7:64254901-64254902
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	chr7:64253690..64256534-chr7:64497237..64499995,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF138-2	chr7:64254766-64254949	NONHSAT121039
2	lnc-ZNF138-2	chr7:64254766-64254949	NONHSAT121040

Variant related genes	Relation type
ENSG00000234585	Chromatin interaction
ENSG00000239985	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10085758	0.82[EUR][1000 genomes]
rs10225171	0.82[ASN][1000 genomes]
rs10279535	0.83[ASN][1000 genomes]
rs10949938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760727	0.82[ASN][1000 genomes]
rs11770219	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1405006	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1464928	0.82[ASN][1000 genomes]
rs1608899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1815167	0.84[CEU][hapmap]
rs1852204	1.00[YRI][hapmap]
rs1880656	0.82[ASN][1000 genomes]
rs2863927	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs3763506	0.82[ASN][1000 genomes]
rs4518551	0.86[ASN][1000 genomes]
rs4717220	0.84[ASN][1000 genomes]
rs4718114	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718125	0.84[ASN][1000 genomes]
rs4718129	0.84[CEU][hapmap]
rs4718131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs55683815	0.86[ASN][1000 genomes]
rs56004721	0.82[ASN][1000 genomes]
rs56075681	0.82[ASN][1000 genomes]
rs57570718	0.82[ASN][1000 genomes]
rs58478503	0.85[AMR][1000 genomes]
rs60939605	0.82[ASN][1000 genomes]
rs61512917	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6460199	0.91[CHB][hapmap]
rs6956129	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6956610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961445	0.86[ASN][1000 genomes]
rs6976546	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73126358	0.84[ASN][1000 genomes]
rs73126387	0.84[ASN][1000 genomes]
rs73130313	0.83[ASN][1000 genomes]
rs73130314	0.83[ASN][1000 genomes]
rs73138788	0.81[AMR][1000 genomes]
rs73138791	0.81[AMR][1000 genomes]
rs73142704	0.85[ASN][1000 genomes]
rs73142715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73142719	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73142749	0.86[ASN][1000 genomes]
rs7781361	0.82[EUR][1000 genomes]
rs7784902	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7805112	0.91[CHB][hapmap]
rs7810067	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
4	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
10	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
13	esv3394685	chr7:64150166-64268675	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
16	nsv888281	chr7:64250409-64295884	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv970857	chr7:64254831-64256462	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs11983033	SEPHS1P1	cis	Stomach	GTEx
rs11983033	SEPHS1P1	cis	Artery Tibial	GTEx
rs11983033	SEPHS1P1	cis	Thyroid	GTEx
rs11983033	RP11-797H7.3	cis	lung	GTEx
rs11983033	RP11-797H7.5	cis	Thyroid	GTEx
rs11983033	ZNF273	cis	lung	GTEx
rs11983033	SEPHS1P1	cis	Nerve Tibial	GTEx
rs11983033	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs11983033	RP11-797H7.3	cis	Artery Aorta	GTEx
rs11983033	RP11-460N20.5	cis	lung	GTEx
rs11983033	RP11-460N20.5	cis	Thyroid	GTEx
rs11983033	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs11983033	RP11-797H7.3	cis	Thyroid	GTEx
rs11983033	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs11983033	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs11983033	RP11-797H7.3	cis	Whole Blood	GTEx
rs11983033	RP11-797H7.3	cis	Artery Tibial	GTEx
rs11983033	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11983033	RP11-797H7.5	cis	lung	GTEx
rs11983033	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs11983033	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs11983033	SEPHS1P1	cis	Adipose Subcutaneous	GTEx
rs11983033	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs11983033	RP11-797H7.3	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64253800-64255600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:64254000-64255200	Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr7:64254200-64255600	Active TSS	Brain Cingulate Gyrus	brain
4	chr7:64254200-64255800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:64254200-64255800	Active TSS	Fetal Muscle Trunk	muscle
6	chr7:64254200-64256200	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr7:64254400-64255000	Active TSS	Primary B cells from cord blood	blood
8	chr7:64254400-64255200	Active TSS	Primary monocytes fromperipheralblood	blood
9	chr7:64254400-64255200	Active TSS	Monocytes-CD14+_RO01746	blood
10	chr7:64254400-64255400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:64254400-64255400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:64254400-64255400	Active TSS	Aorta	Aorta
13	chr7:64254400-64255400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr7:64254400-64255400	Active TSS	Fetal Heart	heart
15	chr7:64254400-64255400	Active TSS	Fetal Lung	lung
16	chr7:64254400-64255400	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr7:64254400-64255400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr7:64254400-64255400	Active TSS	Stomach Smooth Muscle	stomach
19	chr7:64254400-64255400	Active TSS	NH-A	brain
20	chr7:64254400-64255400	Active TSS	Osteobl	bone
21	chr7:64254400-64255600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:64254400-64255600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:64254400-64255600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr7:64254400-64255600	Active TSS	Primary T cells from cord blood	blood
25	chr7:64254400-64255600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:64254400-64255600	Active TSS	Muscle Satellite Cultured Cells	--
27	chr7:64254400-64255600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:64254400-64255600	Active TSS	Brain Angular Gyrus	brain
29	chr7:64254400-64255600	Active TSS	Brain Hippocampus Middle	brain
30	chr7:64254400-64255600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:64254400-64255600	Active TSS	Brain Substantia Nigra	brain
32	chr7:64254400-64255600	Active TSS	Colonic Mucosa	Colon
33	chr7:64254400-64255600	Active TSS	Colon Smooth Muscle	Colon
34	chr7:64254400-64255600	Active TSS	Duodenum Mucosa	Duodenum
35	chr7:64254400-64255600	Active TSS	Fetal Brain Male	brain
36	chr7:64254400-64255600	Active TSS	Fetal Intestine Small	intestine
37	chr7:64254400-64255600	Active TSS	Ovary	ovary
38	chr7:64254400-64255800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:64254400-64255800	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr7:64254400-64255800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:64254400-64255800	Active TSS	Fetal Kidney	kidney
42	chr7:64254400-64255800	Active TSS	Right Atrium	heart
43	chr7:64254400-64255800	Active TSS	Right Ventricle	heart
44	chr7:64254400-64255800	Active TSS	HepG2	liver
45	chr7:64254400-64256000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:64254400-64256000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:64254400-64256000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:64254400-64256000	Active TSS	Rectal Smooth Muscle	rectum
49	chr7:64254400-64256000	Active TSS	Hela-S3	cervix
50	chr7:64254400-64256200	Active TSS	ES-I3 Cell Line	embryonic stem cell

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