Variant report

Variant	rs4875960
Chromosome Location	chr8:1748166-1748167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10097891	0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10100341	0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10105317	0.81[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs10105496	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10481354	0.81[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs11136421	0.87[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs11136424	0.81[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11778824	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs11986414	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs11990386	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12541297	0.81[AMR][1000 genomes]
rs2293977	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2957085	0.87[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs3812477	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs41526952	1.00[ASW][hapmap]
rs4242538	0.94[JPT][hapmap]
rs4242539	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4370560	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4595147	0.81[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4639549	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4875807	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4875958	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4875961	0.85[AMR][1000 genomes]
rs4875962	0.81[AMR][1000 genomes]
rs6558520	0.81[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs6558521	0.81[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs6558522	0.81[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs6558523	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs6558525	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6558527	0.87[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap]
rs6558533	0.87[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6558534	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6558538	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6558541	0.85[AMR][1000 genomes]
rs6986102	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs6993706	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6996586	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7003112	0.81[AMR][1000 genomes]
rs7005592	0.87[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs7005699	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs7008465	0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs7010616	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7013835	0.86[ASN][1000 genomes]
rs7013841	0.86[ASN][1000 genomes]
rs7014327	0.81[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs7015858	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7017381	0.81[AMR][1000 genomes]
rs7460287	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7460972	0.93[JPT][hapmap]
rs7461159	0.81[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs7462693	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7465135	0.94[ASN][1000 genomes]
rs767745	0.86[AMR][1000 genomes]
rs767746	0.84[AMR][1000 genomes]
rs7818406	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs7827009	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7827285	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7836558	0.87[ASN][1000 genomes]
rs7842425	0.81[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs7844748	0.81[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs7845723	0.81[CHB][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap]
rs7846610	0.81[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889697	chr8:1238564-1861971	Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv889707	chr8:1581839-1920461	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv889711	chr8:1591412-1904157	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1034490	chr8:1654716-1782467	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv609527	chr8:1681733-1753497	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
11	nsv870096	chr8:1682851-1767342	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv532892	chr8:1687433-1839578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv2755149	chr8:1689290-1755281	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
14	nsv465275	chr8:1697086-1768004	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
15	nsv609529	chr8:1697086-1768004	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
16	nsv465276	chr8:1701432-1777571	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
17	nsv609530	chr8:1701432-1777571	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
18	nsv609531	chr8:1717036-1965389	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
19	nsv824454	chr8:1740369-1802873	Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1025444	chr8:1743663-1864809	Genic enhancers Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
21	nsv539299	chr8:1743663-1864809	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
22	esv3478462	chr8:1744445-1748843	Genic enhancers Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv3478460	chr8:1745070-1748418	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv3323501	chr8:1746370-1748918	Weak transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	esv17635	chr8:1746416-1748254	Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv470167	chr8:1746949-1886640	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
27	nsv465277	chr8:1746950-1888447	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
28	nsv609533	chr8:1746950-1888447	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
29	nsv889717	chr8:1746950-1924237	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
30	nsv889718	chr8:1748166-1807756	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4875960	CTD-2336O2.1	cis	Artery Tibial	GTEx
rs4875960	CTD-2336O2.1	cis	Nerve Tibial	GTEx
rs4875960	CLN8	cis	parietal	SCAN
rs4875960	CTD-2336O2.1	cis	Muscle Skeletal	GTEx
rs4875960	CTD-2336O2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1736400-1749800	Weak transcription	Liver	Liver
2	chr8:1743800-1748200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr8:1744800-1753000	Weak transcription	Spleen	Spleen
4	chr8:1745000-1749600	Enhancers	Primary B cells from peripheral blood	blood
5	chr8:1745800-1749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:1746400-1748200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:1747000-1748400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:1747000-1748400	Enhancers	Primary B cells from cord blood	blood
9	chr8:1747000-1749200	Enhancers	Fetal Muscle Leg	muscle
10	chr8:1747000-1750000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr8:1747000-1750000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr8:1747400-1750400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:1747400-1761600	Weak transcription	Pancreas	Pancrea
14	chr8:1747600-1749000	Enhancers	Fetal Stomach	stomach
15	chr8:1747600-1749400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr8:1747600-1749800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr8:1747600-1750000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr8:1747800-1748200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:1747800-1748200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:1747800-1748800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:1747800-1749000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr8:1747800-1749000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr8:1747800-1749000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr8:1747800-1749400	Enhancers	Adipose Nuclei	Adipose
25	chr8:1747800-1749400	Enhancers	Ovary	ovary
26	chr8:1747800-1749800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr8:1747800-1749800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr8:1747800-1750000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr8:1747800-1750600	Enhancers	Fetal Heart	heart
30	chr8:1748000-1748200	Enhancers	Left Ventricle	heart
31	chr8:1748000-1748600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr8:1748000-1748600	Enhancers	Aorta	Aorta
33	chr8:1748000-1749000	Enhancers	Fetal Muscle Trunk	muscle
34	chr8:1748000-1749000	Flanking Active TSS	Osteobl	bone

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