Variant report

Variant	rs4242539
Chromosome Location	chr8:1694236-1694237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10087654	0.88[ASN][1000 genomes]
rs10095548	0.82[ASN][1000 genomes]
rs10095696	0.82[ASN][1000 genomes]
rs10097891	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10100341	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10102731	0.88[ASN][1000 genomes]
rs10105317	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10106153	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10109098	0.83[ASN][1000 genomes]
rs10113471	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10481354	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11136421	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11136422	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11136424	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11778824	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12335115	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12335117	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12674711	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13251071	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13256424	0.85[ASN][1000 genomes]
rs13261755	0.97[ASN][1000 genomes]
rs13282161	0.81[ASN][1000 genomes]
rs13540	0.85[ASN][1000 genomes]
rs2293977	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28376731	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2957085	0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2977197	0.84[ASN][1000 genomes]
rs3812477	0.95[JPT][hapmap]
rs4242538	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4370560	0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4372027	0.87[ASN][1000 genomes]
rs4595147	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4639549	0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4875806	0.81[ASN][1000 genomes]
rs4875889	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4875957	0.81[ASN][1000 genomes]
rs4875958	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6558518	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558520	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6558521	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558522	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558523	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558524	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558525	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6558526	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6558527	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6558528	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6558531	0.87[ASN][1000 genomes]
rs6558532	0.87[ASN][1000 genomes]
rs6558533	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6558534	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6558535	0.87[ASN][1000 genomes]
rs6981804	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6982516	0.82[ASN][1000 genomes]
rs6984632	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6986102	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6991773	0.84[ASN][1000 genomes]
rs6991783	0.84[ASN][1000 genomes]
rs6993706	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7000162	0.82[ASN][1000 genomes]
rs7001282	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7005592	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7005699	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7008465	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7014327	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7014823	0.84[ASN][1000 genomes]
rs7015858	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs71499040	0.83[ASN][1000 genomes]
rs730377	0.87[ASN][1000 genomes]
rs730379	0.86[ASN][1000 genomes]
rs7341635	0.85[ASN][1000 genomes]
rs7459507	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7460230	0.91[ASN][1000 genomes]
rs7460287	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7460365	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7460866	0.84[ASN][1000 genomes]
rs7460972	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7461159	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7461259	0.99[ASN][1000 genomes]
rs7461600	0.81[ASN][1000 genomes]
rs7463876	0.88[ASN][1000 genomes]
rs7463879	0.86[ASN][1000 genomes]
rs7818406	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7822816	0.86[ASN][1000 genomes]
rs7827009	0.95[JPT][hapmap]
rs7827285	0.94[JPT][hapmap]
rs7828950	0.88[ASN][1000 genomes]
rs7838456	0.87[ASN][1000 genomes]
rs7842425	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7844748	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7845723	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap]
rs7846610	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9022	0.91[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	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	nsv1031375	chr8:1320657-1722050	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv934075	chr8:1626857-1736355	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv465274	chr8:1685064-1728292	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv609528	chr8:1685064-1728292	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	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
17	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4242539	CTD-2336O2.1	cis	Esophagus Muscularis	GTEx
rs4242539	CTD-2336O2.1	cis	Muscle Skeletal	GTEx
rs4242539	CTD-2336O2.1	cis	Thyroid	GTEx
rs4242539	CTD-2336O2.1	cis	Nerve Tibial	GTEx
rs4242539	CTD-2336O2.1	cis	Artery Tibial	GTEx
rs4242539	CTD-2336O2.1	cis	lung	GTEx
rs4242539	CTD-2336O2.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1692000-1694800	Enhancers	Spleen	Spleen
2	chr8:1692200-1694800	Enhancers	Placenta	Placenta
3	chr8:1692200-1695400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr8:1692200-1695600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr8:1692200-1696200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:1692200-1696400	Enhancers	Primary B cells from peripheral blood	blood
7	chr8:1692400-1694600	Enhancers	Brain Substantia Nigra	brain
8	chr8:1692400-1694800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr8:1692400-1694800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:1692400-1695000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr8:1692400-1695200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:1692400-1695200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr8:1692400-1695400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:1692400-1695400	Enhancers	Stomach Mucosa	stomach
15	chr8:1692600-1695600	Enhancers	Primary hematopoietic stem cells	blood
16	chr8:1692600-1707400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:1693000-1694800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr8:1693000-1695400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:1693000-1695600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:1693200-1694400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr8:1693200-1694400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr8:1693200-1694400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr8:1693200-1694400	Flanking Active TSS	NH-A	brain
24	chr8:1693200-1694800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr8:1693200-1694800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr8:1693200-1694800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr8:1693200-1694800	Flanking Active TSS	GM12878-XiMat	blood
28	chr8:1693200-1694800	Flanking Active TSS	K562	blood
29	chr8:1693200-1695000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr8:1693200-1695000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr8:1693200-1695000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr8:1693200-1695000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr8:1693200-1695000	Enhancers	Fetal Intestine Small	intestine
34	chr8:1693200-1695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr8:1693200-1695200	Enhancers	HUVEC	blood vessel
36	chr8:1693200-1695400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:1693200-1695400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr8:1693400-1694400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr8:1693400-1694600	Enhancers	Pancreas	Pancrea
40	chr8:1693400-1694800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:1693400-1694800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr8:1693400-1694800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr8:1693400-1694800	Enhancers	Fetal Lung	lung
44	chr8:1693400-1694800	Flanking Active TSS	A549	lung
45	chr8:1693400-1695000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr8:1693400-1695000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:1693400-1695000	Enhancers	Fetal Intestine Large	intestine
48	chr8:1693400-1695200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr8:1693400-1695200	Enhancers	Colon Smooth Muscle	Colon
50	chr8:1693400-1695200	Enhancers	NHEK	skin

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