Variant report

Variant	rs6932350
Chromosome Location	chr6:26571629-26571630
allele	A/T
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:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26505484..26507456-chr6:26570527..26573483,2	K562	blood:
2	chr6:26456964..26459608-chr6:26569874..26571893,2	K562	blood:
3	chr6:26320916..26324695-chr6:26568559..26572226,5	K562	blood:
4	chr6:26571513..26576040-chr6:26594296..26598668,8	MCF-7	breast:
5	chr6:26156493..26160609-chr6:26566713..26572551,10	K562	blood:
6	chr6:26569878..26572045-chr6:26757682..26759933,2	K562	blood:
7	chr6:26217011..26219959-chr6:26570720..26572283,2	K562	blood:
8	chr6:26532740..26539448-chr6:26569667..26573975,11	K562	blood:
9	chr6:26571551..26574960-chr6:26589936..26592999,3	MCF-7	breast:
10	chr6:26519454..26523332-chr6:26568814..26573401,9	K562	blood:
11	chr6:26328751..26331113-chr6:26570899..26573999,3	K562	blood:
12	chr6:26532421..26535211-chr6:26570479..26571983,2	MCF-7	breast:
13	chr6:26570796..26573059-chr6:27099737..27102153,2	MCF-7	breast:
14	chr6:26569051..26574263-chr6:27058255..27061104,5	K562	blood:
15	chr6:26566413..26579648-chr6:26592370..26599609,38	K562	blood:
16	chr6:26318750..26323113-chr6:26568559..26574896,7	K562	blood:
17	chr6:26198264..26200984-chr6:26569161..26573441,3	K562	blood:
18	chr6:26536057..26540079-chr6:26569592..26573592,5	K562	blood:
19	chr6:26569658..26573509-chr6:27099375..27102190,3	K562	blood:
20	chr6:26571063..26574475-chr6:27099949..27102316,3	K562	blood:
21	chr6:26570341..26572398-chr6:26986666..26989139,2	K562	blood:
22	chr6:26215231..26219129-chr6:26568240..26572057,4	K562	blood:
23	chr6:26197063..26201170-chr6:26570047..26573982,4	K562	blood:
24	chr6:26567325..26570025-chr6:26570280..26572074,2	MCF-7	breast:
25	chr6:26519760..26523332-chr6:26568841..26572559,5	K562	blood:
26	chr6:26329307..26333799-chr6:26568024..26573999,9	K562	blood:
27	chr6:26340224..26344158-chr6:26569567..26573981,6	K562	blood:
28	chr6:26174601..26176102-chr6:26570982..26573796,2	K562	blood:
29	chr6:26204076..26206640-chr6:26570365..26573810,4	K562	blood:
30	chr6:26156671..26160280-chr6:26569301..26572551,5	K562	blood:
31	chr6:26568882..26571175-chr6:26571456..26572979,2	K562	blood:
32	chr6:26570400..26571983-chr6:27110015..27111671,2	MCF-7	breast:
33	chr6:26570453..26572471-chr6:26595621..26597254,2	MCF-7	breast:
34	chr6:26471319..26475410-chr6:26567164..26571952,5	K562	blood:
35	chr6:26340127..26342724-chr6:26570668..26572890,2	MCF-7	breast:
36	chr6:26568033..26580216-chr6:26588796..26603066,49	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000238621	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000220875	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000112763	Chromatin interaction
ENSG00000224843	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1001687	0.90[EUR][1000 genomes]
rs10214634	0.92[EUR][1000 genomes]
rs10223789	0.85[EUR][1000 genomes]
rs10223792	0.85[EUR][1000 genomes]
rs10484442	0.92[EUR][1000 genomes]
rs1056347	0.82[EUR][1000 genomes]
rs1056667	0.81[EUR][1000 genomes]
rs1056668	0.84[EUR][1000 genomes]
rs1078679	0.93[EUR][1000 genomes]
rs10946834	0.82[EUR][1000 genomes]
rs10946835	0.82[EUR][1000 genomes]
rs10946837	0.91[EUR][1000 genomes]
rs11752946	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11754138	0.82[EUR][1000 genomes]
rs11756120	0.81[EUR][1000 genomes]
rs12526680	0.94[EUR][1000 genomes]
rs12663883	0.89[EUR][1000 genomes]
rs12663894	0.88[EUR][1000 genomes]
rs12665431	0.88[EUR][1000 genomes]
rs1321480	0.82[EUR][1000 genomes]
rs1321481	0.87[EUR][1000 genomes]
rs1321482	0.89[EUR][1000 genomes]
rs1535276	0.82[EUR][1000 genomes]
rs1535277	0.86[EUR][1000 genomes]
rs1570059	0.90[EUR][1000 genomes]
rs1570060	0.90[EUR][1000 genomes]
rs1570061	0.89[EUR][1000 genomes]
rs1884946	0.90[EUR][1000 genomes]
rs1884947	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1884948	0.93[EUR][1000 genomes]
rs1884949	0.93[EUR][1000 genomes]
rs1977201	0.90[EUR][1000 genomes]
rs2208331	0.81[EUR][1000 genomes]
rs2224380	0.92[EUR][1000 genomes]
rs2393670	0.88[EUR][1000 genomes]
rs35355150	0.83[EUR][1000 genomes]
rs4573	0.93[EUR][1000 genomes]
rs4713006	0.82[EUR][1000 genomes]
rs4713008	0.87[EUR][1000 genomes]
rs4871	0.90[EUR][1000 genomes]
rs55930917	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6456733	0.92[EUR][1000 genomes]
rs6456734	0.92[EUR][1000 genomes]
rs6456735	0.90[EUR][1000 genomes]
rs6909277	0.87[EUR][1000 genomes]
rs6910899	0.82[EUR][1000 genomes]
rs6910930	0.82[EUR][1000 genomes]
rs6913398	0.90[EUR][1000 genomes]
rs6913462	0.89[EUR][1000 genomes]
rs6913877	0.89[EUR][1000 genomes]
rs6918360	0.89[EUR][1000 genomes]
rs6918506	0.89[EUR][1000 genomes]
rs6918854	0.89[EUR][1000 genomes]
rs6922824	0.92[EUR][1000 genomes]
rs6924838	0.93[EUR][1000 genomes]
rs6924865	0.81[EUR][1000 genomes]
rs6925703	0.82[EUR][1000 genomes]
rs6925783	0.91[EUR][1000 genomes]
rs6925895	0.93[EUR][1000 genomes]
rs6930120	0.91[EUR][1000 genomes]
rs6932156	0.93[EUR][1000 genomes]
rs6932865	0.90[EUR][1000 genomes]
rs6933176	0.90[EUR][1000 genomes]
rs6940053	0.92[EUR][1000 genomes]
rs6940188	0.92[EUR][1000 genomes]
rs6941022	0.92[EUR][1000 genomes]
rs767471	0.92[EUR][1000 genomes]
rs9295694	0.81[EUR][1000 genomes]
rs9295695	0.82[EUR][1000 genomes]
rs9295698	0.92[EUR][1000 genomes]
rs9357010	0.82[EUR][1000 genomes]
rs9358954	0.81[EUR][1000 genomes]
rs9379887	0.80[EUR][1000 genomes]
rs9393729	0.81[EUR][1000 genomes]
rs9393731	0.82[EUR][1000 genomes]
rs9393732	0.82[EUR][1000 genomes]
rs9461267	0.81[EUR][1000 genomes]
rs9461270	0.90[EUR][1000 genomes]
rs9461271	0.92[EUR][1000 genomes]
rs9461272	0.85[EUR][1000 genomes]
rs9467773	0.81[EUR][1000 genomes]
rs9467775	0.81[EUR][1000 genomes]
rs9467776	0.81[EUR][1000 genomes]
rs9467778	0.88[EUR][1000 genomes]
rs9467779	0.88[EUR][1000 genomes]
rs9467782	0.90[EUR][1000 genomes]
rs9467783	0.90[EUR][1000 genomes]
rs9467784	0.90[EUR][1000 genomes]
rs9467787	0.92[EUR][1000 genomes]
rs9467791	0.92[EUR][1000 genomes]
rs9467796	0.93[EUR][1000 genomes]
rs9467797	0.93[EUR][1000 genomes]
rs9467798	0.89[EUR][1000 genomes]
rs9467799	0.86[EUR][1000 genomes]
rs9467800	0.86[EUR][1000 genomes]
rs9467802	0.85[EUR][1000 genomes]
rs9986382	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6932350	HMGN4	cis	Whole Blood	GTEx
rs6932350	RP11-457M11.5	cis	Artery Tibial	GTEx
rs6932350	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs6932350	HMGN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26569600-26571800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:26569600-26571800	Weak transcription	HepG2	liver
3	chr6:26569600-26571800	Weak transcription	HSMM	muscle
4	chr6:26569600-26572000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:26569600-26572000	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:26569600-26572000	Weak transcription	Esophagus	oesophagus
7	chr6:26569600-26572000	Weak transcription	Ovary	ovary
8	chr6:26569600-26572000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:26569600-26572000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:26569600-26572000	Weak transcription	Right Ventricle	heart
11	chr6:26569600-26572000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:26569600-26572000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:26569600-26572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:26569600-26572200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:26569600-26572200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:26569600-26572200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:26569600-26572200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:26569600-26572200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:26569600-26572200	Weak transcription	Aorta	Aorta
20	chr6:26569600-26572200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:26569600-26572200	Weak transcription	Colonic Mucosa	Colon
22	chr6:26569600-26572200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:26569600-26572200	Weak transcription	Fetal Lung	lung
24	chr6:26569600-26572200	Weak transcription	Pancreas	Pancrea
25	chr6:26569600-26572200	Weak transcription	HSMMtube	muscle
26	chr6:26569600-26572400	Weak transcription	Small Intestine	intestine
27	chr6:26569600-26577600	Weak transcription	Spleen	Spleen
28	chr6:26569800-26571800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:26569800-26571800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:26569800-26571800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:26569800-26571800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:26569800-26571800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:26569800-26571800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:26569800-26571800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:26569800-26571800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:26569800-26571800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:26569800-26571800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:26569800-26571800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:26569800-26571800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:26569800-26571800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:26569800-26571800	Weak transcription	Brain Anterior Caudate	brain
42	chr6:26569800-26571800	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:26569800-26571800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:26569800-26571800	Weak transcription	Fetal Heart	heart
45	chr6:26569800-26571800	Weak transcription	NHDF-Ad	bronchial
46	chr6:26569800-26572000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:26569800-26572000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:26569800-26572000	Weak transcription	Primary B cells from cord blood	blood
49	chr6:26569800-26572000	Weak transcription	Primary T cells from cord blood	blood
50	chr6:26569800-26572000	Weak transcription	Primary T cells fromperipheralblood	blood

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