Variant report

Variant	rs9467778
Chromosome Location	chr6:26534743-26534744
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26311628..26314659-chr6:26531812..26534780,3	K562	blood:
2	chr6:26421115..26423072-chr6:26532607..26534934,2	K562	blood:
3	chr6:26533371..26536104-chr6:27090402..27093172,2	K562	blood:
4	chr6:26532421..26535211-chr6:26570479..26571983,2	MCF-7	breast:
5	chr6:26215522..26217770-chr6:26533017..26534753,2	K562	blood:
6	chr6:26521097..26522771-chr6:26534272..26536391,2	MCF-7	breast:
7	chr6:26520237..26523197-chr6:26533292..26535443,5	MCF-7	breast:
8	chr6:26318172..26320821-chr6:26533523..26535253,2	K562	blood:
9	chr6:26199047..26200961-chr6:26534611..26536638,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187990	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000124549	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000272468	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1001687	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10214634	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10223789	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10223792	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10484442	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1056347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056667	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1056668	0.87[EUR][1000 genomes]
rs1078679	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10946834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10946835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10946837	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11752946	0.89[EUR][1000 genomes]
rs11754138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11756120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526680	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12663883	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12663894	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12665431	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1321479	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1321481	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321482	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1535274	0.81[AMR][1000 genomes]
rs1535276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535277	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1570059	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1570060	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1570061	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1884946	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1884947	0.90[EUR][1000 genomes]
rs1884948	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1884949	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1977201	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2208331	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2224380	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2255070	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393669	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2393670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28558133	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35355150	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736781	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736782	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757151	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4343916	0.81[AMR][1000 genomes]
rs4368798	0.80[AFR][1000 genomes]
rs4573	0.92[EUR][1000 genomes]
rs4713006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55930917	0.88[EUR][1000 genomes]
rs6456733	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6456734	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6456735	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6903973	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6909277	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6910899	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913398	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6913462	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6913877	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6918360	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6918506	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6918854	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6922824	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6924838	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6924865	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6925047	0.81[AMR][1000 genomes]
rs6925703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925783	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6925895	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6926629	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930120	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6932156	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6932350	0.88[EUR][1000 genomes]
rs6932865	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6933176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940053	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6940188	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6941022	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs767471	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7753565	0.81[EUR][1000 genomes]
rs9295694	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295698	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9357010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9358952	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379887	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393728	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393729	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461259	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461267	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461270	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9461271	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9461272	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9461275	0.80[AFR][1000 genomes]
rs9467773	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9467774	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9467775	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467776	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467782	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467783	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467784	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467787	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9467791	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9467796	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9467797	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9467798	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9467799	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9467800	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9467802	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9467805	0.81[AFR][1000 genomes]
rs9986382	0.96[AFR][1000 genomes];0.96[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	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9467778	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs9467778	ZNF322	cis	Nerve Tibial	GTEx
rs9467778	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs9467778	HMGN4	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26532800-26535000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:26533600-26535800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:26533600-26536800	Weak transcription	Stomach Mucosa	stomach
4	chr6:26533800-26534800	Weak transcription	Psoas Muscle	Psoas
5	chr6:26533800-26535000	Weak transcription	Colonic Mucosa	Colon
6	chr6:26533800-26535000	Weak transcription	Fetal Lung	lung
7	chr6:26533800-26535600	Enhancers	Brain Angular Gyrus	brain
8	chr6:26533800-26535800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:26533800-26535800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:26533800-26536200	Weak transcription	Placenta	Placenta
11	chr6:26533800-26536400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:26533800-26536400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:26533800-26536600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:26533800-26536800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:26533800-26536800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:26533800-26536800	Weak transcription	Aorta	Aorta
17	chr6:26533800-26536800	Weak transcription	Liver	Liver
18	chr6:26533800-26536800	Weak transcription	Lung	lung
19	chr6:26533800-26536800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:26533800-26536800	Weak transcription	Small Intestine	intestine
21	chr6:26533800-26537000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:26533800-26537000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:26533800-26537000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:26533800-26537000	Weak transcription	Esophagus	oesophagus
25	chr6:26533800-26537000	Weak transcription	Left Ventricle	heart
26	chr6:26533800-26537000	Weak transcription	Ovary	ovary
27	chr6:26533800-26537000	Weak transcription	Pancreas	Pancrea
28	chr6:26533800-26537000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:26534000-26534800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:26534000-26534800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:26534000-26534800	Weak transcription	Fetal Thymus	thymus
32	chr6:26534000-26535000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:26534000-26535000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:26534000-26535000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:26534000-26535000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:26534000-26535000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:26534000-26535000	Enhancers	Primary B cells from cord blood	blood
38	chr6:26534000-26535000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:26534000-26535000	Weak transcription	Brain Anterior Caudate	brain
40	chr6:26534000-26535000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:26534000-26535000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr6:26534000-26535000	Weak transcription	HSMMtube	muscle
43	chr6:26534000-26535200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:26534000-26535400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:26534000-26535800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:26534000-26536000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:26534000-26536200	Weak transcription	HUVEC	blood vessel
48	chr6:26534000-26536400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:26534000-26536400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:26534000-26536400	Weak transcription	Adipose Nuclei	Adipose

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