Variant report

Variant	rs6460195
Chromosome Location	chr7:64292695-64292696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF138-2	chr7:64291829-64294059	NONHSAT121040

Extended variants
information (count: 81 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10225171	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10240146	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10279535	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10949938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs10949946	0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs10949947	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10949948	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs11760270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs11760727	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974982	0.81[AMR][1000 genomes]
rs11983033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13226426	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13228575	0.82[EUR][1000 genomes]
rs13230564	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1464927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815167	0.84[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs1880656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863927	0.83[CEU][hapmap];0.95[GIH][hapmap]
rs3763506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273744	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4392773	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4518551	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717217	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4717220	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718122	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4718125	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718129	0.84[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs4718131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683815	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55780785	0.86[ASN][1000 genomes]
rs56004721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075681	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56391048	0.85[ASN][1000 genomes]
rs56785930	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57570718	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59666562	0.84[ASN][1000 genomes]
rs60779365	0.86[ASN][1000 genomes]
rs61703184	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6460199	0.91[CHB][hapmap]
rs67686910	0.86[ASN][1000 genomes]
rs6956129	1.00[CEU][hapmap]
rs6956610	0.82[ASN][1000 genomes]
rs6961445	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6976546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs73126358	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73126387	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130313	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73130314	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73132347	0.85[ASN][1000 genomes]
rs73132368	0.86[ASN][1000 genomes]
rs73132377	0.86[ASN][1000 genomes]
rs73142715	0.82[ASN][1000 genomes]
rs73142749	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7784902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7785735	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7787287	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7788090	0.86[ASN][1000 genomes]
rs7789149	0.80[EUR][1000 genomes]
rs7790203	0.81[EUR][1000 genomes]
rs7792444	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7793057	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7805112	0.91[CHB][hapmap]
rs7808498	0.85[ASN][1000 genomes]
rs7809177	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7810067	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs6460195	RP11-797H7.3	cis	Artery Tibial	GTEx
rs6460195	RP11-797H7.3	cis	lung	GTEx
rs6460195	SEPHS1P1	cis	Nerve Tibial	GTEx
rs6460195	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs6460195	RP11-797H7.3	cis	Artery Aorta	GTEx
rs6460195	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs6460195	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460195	SEPHS1P1	cis	Stomach	GTEx
rs6460195	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs6460195	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs6460195	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs6460195	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs6460195	RP11-797H7.3	cis	Thyroid	GTEx
rs6460195	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs6460195	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs6460195	RP11-797H7.3	cis	Esophagus Muscularis	GTEx
rs6460195	SEPHS1P1	cis	Artery Tibial	GTEx
rs6460195	RP11-797H7.5	cis	Thyroid	GTEx
rs6460195	CCT6P3	cis	Esophagus Mucosa	GTEx
rs6460195	RP11-797H7.5	cis	lung	GTEx
rs6460195	SEPHS1P1	cis	Thyroid	GTEx
rs6460195	INTS4L1	cis	Adipose Subcutaneous	GTEx
rs6460195	RP11-797H7.3	cis	Stomach	GTEx
rs6460195	RP11-797H7.3	cis	Whole Blood	GTEx
rs6460195	RP11-460N20.5	cis	Thyroid	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64255800-64293200	Weak transcription	NH-A	brain
2	chr7:64255800-64293400	Weak transcription	Psoas Muscle	Psoas
3	chr7:64256000-64294400	Weak transcription	Fetal Kidney	kidney
4	chr7:64261000-64295400	Weak transcription	Osteobl	bone
5	chr7:64268600-64296000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:64268800-64293400	Weak transcription	Brain Angular Gyrus	brain
7	chr7:64272400-64292800	Weak transcription	Brain Anterior Caudate	brain
8	chr7:64272800-64295200	Weak transcription	Fetal Thymus	thymus
9	chr7:64273000-64292800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:64273400-64301400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:64275600-64294000	Weak transcription	Fetal Brain Male	brain
12	chr7:64278000-64293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:64284600-64295800	Weak transcription	Brain Germinal Matrix	brain
14	chr7:64284800-64293000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:64284800-64293000	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:64284800-64294200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:64284800-64299800	Weak transcription	Pancreas	Pancrea
18	chr7:64285400-64296400	Weak transcription	Left Ventricle	heart
19	chr7:64286000-64293200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:64290200-64293000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:64290400-64293000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr7:64290400-64293400	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr7:64290800-64293400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr7:64291000-64292800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:64291000-64292800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
26	chr7:64291200-64292800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
27	chr7:64291200-64292800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:64291200-64293200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:64291200-64293400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:64291400-64292800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr7:64291400-64292800	Strong transcription	Liver	Liver
32	chr7:64291400-64292800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr7:64291400-64293000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:64291400-64293200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:64291400-64293400	Strong transcription	Adipose Nuclei	Adipose
36	chr7:64291400-64293600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr7:64291600-64294200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr7:64291600-64296000	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:64291800-64293000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:64291800-64293200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr7:64291800-64293200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:64291800-64293600	Strong transcription	HSMM	muscle
43	chr7:64291800-64293800	Weak transcription	Fetal Intestine Large	intestine
44	chr7:64292000-64293600	ZNF genes & repeats	Primary B cells from cord blood	blood
45	chr7:64292200-64293000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:64292200-64293200	Enhancers	Rectal Smooth Muscle	rectum
47	chr7:64292200-64293400	ZNF genes & repeats	Dnd41	blood
48	chr7:64292200-64294800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:64292400-64292800	Strong transcription	Ovary	ovary
50	chr7:64292400-64293200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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