Variant report

Variant	rs55930917
Chromosome Location	chr6:26577186-26577187
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26215403..26219104-chr6:26575436..26578957,4	K562	blood:
2	chr6:26575145..26580691-chr6:26582301..26587887,10	K562	blood:
3	chr6:26216001..26219242-chr6:26574102..26578957,5	K562	blood:
4	chr6:26195366..26197728-chr6:26574483..26577323,2	K562	blood:
5	chr6:26327970..26330676-chr6:26575820..26578738,2	K562	blood:
6	chr6:26575403..26577801-chr6:26599976..26601665,3	K562	blood:
7	chr6:26576709..26579469-chr6:26595010..26597747,2	MCF-7	breast:
8	chr6:26575952..26578920-chr6:26582301..26585861,4	K562	blood:
9	chr6:26566413..26579648-chr6:26592370..26599609,38	K562	blood:
10	chr6:26520128..26522932-chr6:26576156..26579285,4	K562	blood:
11	chr6:26308793..26311615-chr6:26576648..26578287,2	K562	blood:
12	chr6:26341150..26343678-chr6:26575652..26577197,2	K562	blood:
13	chr6:26576770..26577438-chr6:26595189..26595697,2	K562	blood:
14	chr6:26575954..26578514-chr6:27111915..27114661,2	K562	blood:
15	chr6:26576158..26578683-chr6:27099793..27101418,3	K562	blood:
16	chr6:26535611..26540047-chr6:26576394..26579600,4	K562	blood:
17	chr6:26285889..26287811-chr6:26576369..26578960,2	K562	blood:
18	chr6:26541729..26543411-chr6:26576160..26577936,2	K562	blood:
19	chr6:26568033..26580216-chr6:26588796..26603066,49	K562	blood:
20	chr6:26402744..26404382-chr6:26575217..26577628,2	K562	blood:
21	chr6:26536620..26538867-chr6:26576288..26578360,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000216331	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1001687	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10214634	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10223789	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10223792	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1027203	0.81[AFR][1000 genomes]
rs10484442	0.92[EUR][1000 genomes]
rs1056347	0.84[EUR][1000 genomes]
rs1056667	0.82[EUR][1000 genomes]
rs1078679	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10946834	0.84[EUR][1000 genomes]
rs10946835	0.84[EUR][1000 genomes]
rs10946837	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11752946	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11754138	0.84[EUR][1000 genomes]
rs11756120	0.83[EUR][1000 genomes]
rs12526680	0.88[EUR][1000 genomes]
rs12663883	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12663894	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12665431	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13207371	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1321479	0.81[EUR][1000 genomes]
rs1321480	0.84[EUR][1000 genomes]
rs1321481	0.87[EUR][1000 genomes]
rs1321482	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1535276	0.84[EUR][1000 genomes]
rs1535277	0.85[EUR][1000 genomes]
rs1570059	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1570060	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1570061	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1884946	0.90[EUR][1000 genomes]
rs1884947	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1884948	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1884949	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1977201	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2172007	0.81[AFR][1000 genomes]
rs2208331	0.82[EUR][1000 genomes]
rs2224380	0.92[EUR][1000 genomes]
rs2255070	0.81[EUR][1000 genomes]
rs2393670	0.88[EUR][1000 genomes]
rs35355150	0.85[EUR][1000 genomes]
rs3736781	0.81[EUR][1000 genomes]
rs3736782	0.81[EUR][1000 genomes]
rs4573	0.87[EUR][1000 genomes]
rs4713006	0.84[EUR][1000 genomes]
rs4713008	0.87[EUR][1000 genomes]
rs4871	0.90[EUR][1000 genomes]
rs6456733	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6456734	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6456735	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6903973	0.81[EUR][1000 genomes]
rs6909277	0.87[EUR][1000 genomes]
rs6910899	0.84[EUR][1000 genomes]
rs6910930	0.84[EUR][1000 genomes]
rs6913398	0.90[EUR][1000 genomes]
rs6913462	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6913877	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918360	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918506	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918854	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922824	0.92[EUR][1000 genomes]
rs6924838	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6924865	0.83[EUR][1000 genomes]
rs6925703	0.84[EUR][1000 genomes]
rs6925783	0.91[EUR][1000 genomes]
rs6925895	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6926629	0.81[EUR][1000 genomes]
rs6930120	0.91[EUR][1000 genomes]
rs6932156	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6932350	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6932865	0.90[EUR][1000 genomes]
rs6933176	0.90[EUR][1000 genomes]
rs6940053	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940188	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6941022	0.92[EUR][1000 genomes]
rs767471	0.92[EUR][1000 genomes]
rs9295694	0.82[EUR][1000 genomes]
rs9295695	0.84[EUR][1000 genomes]
rs9295698	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9357010	0.84[EUR][1000 genomes]
rs9358954	0.83[EUR][1000 genomes]
rs9379887	0.82[EUR][1000 genomes]
rs9393729	0.82[EUR][1000 genomes]
rs9393731	0.84[EUR][1000 genomes]
rs9393732	0.84[EUR][1000 genomes]
rs9461259	0.81[EUR][1000 genomes]
rs9461267	0.83[EUR][1000 genomes]
rs9461270	0.90[EUR][1000 genomes]
rs9461271	0.92[EUR][1000 genomes]
rs9461272	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9467774	0.81[EUR][1000 genomes]
rs9467775	0.82[EUR][1000 genomes]
rs9467776	0.82[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];0.81[ASN][1000 genomes]
rs9467796	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9467797	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9467798	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467799	0.95[EUR][1000 genomes]
rs9467800	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9467802	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9986382	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv3475110	chr6:26575704-26577436	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3475111	chr6:26575704-26577436	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55930917	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs55930917	HCG11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26569600-26577600	Weak transcription	Spleen	Spleen
2	chr6:26573000-26577200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:26573000-26577600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:26573200-26577400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:26573400-26577200	Weak transcription	Dnd41	blood
6	chr6:26573400-26577400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:26573400-26577400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:26573400-26577400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:26575600-26578600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:26575800-26577400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:26575800-26578200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:26575800-26578400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:26575800-26578400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr6:26575800-26578400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:26575800-26578600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:26575800-26578600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:26576000-26577200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:26576000-26577200	Flanking Active TSS	HepG2	liver
19	chr6:26576000-26578200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:26576000-26578200	Active TSS	A549	lung
21	chr6:26576600-26577200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:26576600-26577600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:26576600-26577800	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:26576600-26578000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:26576600-26578000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:26576600-26578000	Flanking Active TSS	NHEK	skin
27	chr6:26576600-26578200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:26576600-26578200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:26576600-26578400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:26576800-26577200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr6:26576800-26577200	Bivalent Enhancer	Primary T cells from cord blood	blood
32	chr6:26576800-26577200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
33	chr6:26576800-26577200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:26576800-26577200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
35	chr6:26576800-26577200	Bivalent/Poised TSS	NHDF-Ad	bronchial
36	chr6:26576800-26577400	Active TSS	Osteobl	bone
37	chr6:26576800-26577600	Active TSS	Brain Angular Gyrus	brain
38	chr6:26576800-26577600	Active TSS	Psoas Muscle	Psoas
39	chr6:26576800-26577800	Active TSS	Brain Anterior Caudate	brain
40	chr6:26576800-26577800	Bivalent Enhancer	Fetal Thymus	thymus
41	chr6:26576800-26577800	Active TSS	Right Atrium	heart
42	chr6:26576800-26578000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:26576800-26578000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr6:26576800-26578000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr6:26576800-26578000	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr6:26576800-26578000	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr6:26576800-26578000	Bivalent Enhancer	Fetal Intestine Small	intestine
48	chr6:26576800-26578000	Flanking Active TSS	GM12878-XiMat	blood
49	chr6:26576800-26578000	Active TSS	NH-A	brain
50	chr6:26576800-26578200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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