Variant report

Variant	rs7461259
Chromosome Location	chr8:1692962-1692963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:1692503..1695228-chr8:1698804..1700487,2	K562	blood:
2	chr8:1690345..1695334-chr8:1710001..1714375,16	MCF-7	breast:
3	chr8:1686398..1691493-chr8:1692732..1695929,5	MCF-7	breast:
4	chr8:1692125..1694169-chr8:1767018..1769382,2	MCF-7	breast:
5	chr8:1682754..1684809-chr8:1691291..1693773,2	MCF-7	breast:
6	chr8:1692732..1694940-chr8:1731254..1732794,2	MCF-7	breast:
7	chr8:1690830..1693396-chr8:1731671..1734648,2	K562	blood:
8	chr8:1692017..1693877-chr8:1696631..1699350,2	MCF-7	breast:
9	chr8:1691117..1696538-chr8:1710667..1714961,13	MCF-7	breast:
10	chr8:1691840..1698609-chr8:1701330..1706354,17	MCF-7	breast:
11	chr8:1691178..1695166-chr8:1727484..1730315,3	MCF-7	breast:
12	chr8:1692167..1695898-chr8:1702417..1705508,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000182372	Chromatin interaction
ENSG00000253982	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10087654	0.89[ASN][1000 genomes]
rs10095548	0.83[ASN][1000 genomes]
rs10095696	0.83[ASN][1000 genomes]
rs10097891	0.85[ASN][1000 genomes]
rs10100341	0.85[ASN][1000 genomes]
rs10102731	0.89[ASN][1000 genomes]
rs10105317	0.94[ASN][1000 genomes]
rs10106153	0.94[ASN][1000 genomes]
rs10109098	0.84[ASN][1000 genomes]
rs10113471	0.98[ASN][1000 genomes]
rs10481354	0.89[ASN][1000 genomes]
rs11136421	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11136422	0.99[ASN][1000 genomes]
rs11136424	0.84[ASN][1000 genomes]
rs11778824	0.83[ASN][1000 genomes]
rs12335115	0.96[ASN][1000 genomes]
rs12335117	0.83[ASN][1000 genomes]
rs12674711	0.93[ASN][1000 genomes]
rs13251071	0.97[ASN][1000 genomes]
rs13256424	0.86[ASN][1000 genomes]
rs13261755	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13282161	0.82[ASN][1000 genomes]
rs13540	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2293977	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28376731	0.91[ASN][1000 genomes]
rs2957085	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2977197	0.85[ASN][1000 genomes]
rs35062922	0.81[ASN][1000 genomes]
rs4242538	1.00[ASN][1000 genomes]
rs4370560	0.88[ASN][1000 genomes]
rs4372027	0.88[ASN][1000 genomes]
rs4595147	0.86[ASN][1000 genomes]
rs4639549	0.88[ASN][1000 genomes]
rs4875806	0.82[ASN][1000 genomes]
rs4875889	0.98[ASN][1000 genomes]
rs4875957	0.82[ASN][1000 genomes]
rs4875958	0.82[ASN][1000 genomes]
rs4876133	0.80[ASN][1000 genomes]
rs6558518	0.94[ASN][1000 genomes]
rs6558520	0.95[ASN][1000 genomes]
rs6558521	0.94[ASN][1000 genomes]
rs6558522	0.94[ASN][1000 genomes]
rs6558523	0.94[ASN][1000 genomes]
rs6558524	0.94[ASN][1000 genomes]
rs6558525	0.94[ASN][1000 genomes]
rs6558526	0.92[ASN][1000 genomes]
rs6558527	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6558528	0.93[ASN][1000 genomes]
rs6558530	0.81[ASN][1000 genomes]
rs6558531	0.88[ASN][1000 genomes]
rs6558532	0.88[ASN][1000 genomes]
rs6558533	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6558534	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6558535	0.88[ASN][1000 genomes]
rs6981804	0.94[ASN][1000 genomes]
rs6982516	0.83[ASN][1000 genomes]
rs6984632	0.91[ASN][1000 genomes]
rs6986102	0.93[ASN][1000 genomes]
rs6991773	0.85[ASN][1000 genomes]
rs6991783	0.85[ASN][1000 genomes]
rs6993706	0.82[ASN][1000 genomes]
rs7000162	0.83[ASN][1000 genomes]
rs7001282	0.94[ASN][1000 genomes]
rs7005592	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7005699	0.94[ASN][1000 genomes]
rs7008465	0.86[ASN][1000 genomes]
rs7014327	0.85[ASN][1000 genomes]
rs7014823	0.85[ASN][1000 genomes]
rs7015858	0.85[ASN][1000 genomes]
rs71499040	0.84[ASN][1000 genomes]
rs730377	0.88[ASN][1000 genomes]
rs730379	0.87[ASN][1000 genomes]
rs7341635	0.86[ASN][1000 genomes]
rs7459507	0.93[ASN][1000 genomes]
rs7460230	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7460287	0.88[ASN][1000 genomes]
rs7460365	0.95[ASN][1000 genomes]
rs7460866	0.85[ASN][1000 genomes]
rs7460972	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7461159	0.84[ASN][1000 genomes]
rs7461600	0.82[ASN][1000 genomes]
rs7463876	0.89[ASN][1000 genomes]
rs7463879	0.87[ASN][1000 genomes]
rs7465178	0.80[ASN][1000 genomes]
rs7818406	0.94[ASN][1000 genomes]
rs7822816	0.87[ASN][1000 genomes]
rs7828950	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7838456	0.88[ASN][1000 genomes]
rs7842425	0.89[ASN][1000 genomes]
rs7844748	0.94[ASN][1000 genomes]
rs7846610	0.89[ASN][1000 genomes]
rs9022	0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7461259	CTD-2336O2.1	cis	Muscle Skeletal	GTEx
rs7461259	CTD-2336O2.1	cis	Adipose Subcutaneous	GTEx
rs7461259	CTD-2336O2.1	cis	Nerve Tibial	GTEx
rs7461259	CTD-2336O2.1	cis	Thyroid	GTEx
rs7461259	CTD-2336O2.1	cis	Artery Tibial	GTEx
rs7461259	CTD-2336O2.1	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1691000-1693000	Weak transcription	K562	blood
2	chr8:1691600-1693200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr8:1691600-1693400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr8:1692000-1694000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr8:1692000-1694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:1692000-1694200	Enhancers	Esophagus	oesophagus
7	chr8:1692000-1694800	Enhancers	Spleen	Spleen
8	chr8:1692200-1693200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr8:1692200-1694800	Enhancers	Placenta	Placenta
10	chr8:1692200-1695400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr8:1692200-1695600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:1692200-1696200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr8:1692200-1696400	Enhancers	Primary B cells from peripheral blood	blood
14	chr8:1692400-1693000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:1692400-1693400	Enhancers	Duodenum Mucosa	Duodenum
16	chr8:1692400-1693600	Enhancers	Gastric	stomach
17	chr8:1692400-1693800	Enhancers	Primary B cells from cord blood	blood
18	chr8:1692400-1694600	Enhancers	Brain Substantia Nigra	brain
19	chr8:1692400-1694800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr8:1692400-1694800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr8:1692400-1695000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr8:1692400-1695200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr8:1692400-1695200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr8:1692400-1695400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:1692400-1695400	Enhancers	Stomach Mucosa	stomach
26	chr8:1692600-1693200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr8:1692600-1693200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr8:1692600-1693200	Weak transcription	Colonic Mucosa	Colon
29	chr8:1692600-1693200	Enhancers	NH-A	brain
30	chr8:1692600-1693200	Enhancers	NHLF	lung
31	chr8:1692600-1693400	Weak transcription	Brain Anterior Caudate	brain
32	chr8:1692600-1693400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr8:1692600-1693800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr8:1692600-1693800	Weak transcription	Right Atrium	heart
35	chr8:1692600-1695600	Enhancers	Primary hematopoietic stem cells	blood
36	chr8:1692600-1707400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr8:1692800-1693400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr8:1692800-1693600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr8:1692800-1693800	Weak transcription	Adipose Nuclei	Adipose
40	chr8:1692800-1693800	Weak transcription	Lung	lung
41	chr8:1692800-1693800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr8:1692800-1693800	Enhancers	HepG2	liver

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