Variant report

Variant	rs9468140
Chromosome Location	chr6:27471515-27471516
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27471243..27473118-chr6:27473124..27475261,2	K562	blood:
2	chr6:27438047..27443464-chr6:27468935..27473821,5	K562	blood:
3	chr6:27439182..27442586-chr6:27469972..27473821,4	K562	blood:
4	chr6:27470088..27471608-chr6:27487269..27490005,2	K562	blood:
5	chr6:27468932..27472099-chr6:27510680..27513985,4	K562	blood:
6	chr6:27469986..27472017-chr6:27494053..27495560,2	K562	blood:
7	chr6:27246689..27248235-chr6:27471061..27472796,2	K562	blood:
8	chr6:27099480..27102388-chr6:27469674..27472608,2	K562	blood:
9	chr6:27443641..27445156-chr6:27470479..27473183,2	K562	blood:
10	chr6:27470766..27473245-chr6:27617195..27618782,2	K562	blood:
11	chr6:27112845..27117785-chr6:27470908..27475349,7	K562	blood:
12	chr6:27470846..27472818-chr6:27518187..27522174,4	K562	blood:
13	chr6:27470257..27473411-chr6:27494053..27498486,4	K562	blood:
14	chr6:27445186..27449983-chr6:27468978..27472948,6	K562	blood:
15	chr6:27469947..27474974-chr6:27485508..27488698,9	K562	blood:
16	chr6:27143119..27145286-chr6:27470230..27472142,2	K562	blood:
17	chr6:27258318..27260398-chr6:27469283..27471523,2	K562	blood:
18	chr6:27471116..27473574-chr6:27483046..27485939,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000270666	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1014227	0.92[ASN][1000 genomes]
rs10452601	0.97[ASN][1000 genomes]
rs10484398	0.92[ASN][1000 genomes]
rs10807024	0.92[ASN][1000 genomes]
rs10807025	0.92[ASN][1000 genomes]
rs10946919	0.89[ASN][1000 genomes]
rs10946920	0.92[ASN][1000 genomes]
rs10946921	0.92[ASN][1000 genomes]
rs10946931	0.98[ASN][1000 genomes]
rs10946932	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10946933	0.99[ASN][1000 genomes]
rs11970336	0.92[ASN][1000 genomes]
rs12199110	0.91[ASN][1000 genomes]
rs12206045	0.97[ASN][1000 genomes]
rs12213598	0.92[ASN][1000 genomes]
rs12215117	0.92[ASN][1000 genomes]
rs12524409	0.92[ASN][1000 genomes]
rs12529839	0.91[ASN][1000 genomes]
rs13201443	0.92[ASN][1000 genomes]
rs13201965	0.92[ASN][1000 genomes]
rs13201985	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13212050	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13215560	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13217162	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13217248	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13220155	0.92[ASN][1000 genomes]
rs1883216	0.92[ASN][1000 genomes]
rs2049944	0.92[ASN][1000 genomes]
rs2049945	0.92[ASN][1000 genomes]
rs2092120	0.88[ASN][1000 genomes]
rs2092121	0.92[ASN][1000 genomes]
rs2092122	0.92[ASN][1000 genomes]
rs2103557	0.86[ASN][1000 genomes]
rs2142705	0.92[ASN][1000 genomes]
rs2179154	0.92[ASN][1000 genomes]
rs2205831	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235252	0.91[ASN][1000 genomes]
rs2235254	0.91[ASN][1000 genomes]
rs2272814	0.92[ASN][1000 genomes]
rs2272815	0.90[ASN][1000 genomes]
rs2272816	0.92[ASN][1000 genomes]
rs2294308	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294309	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2893917	0.92[ASN][1000 genomes]
rs35394453	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4478400	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4711153	0.92[ASN][1000 genomes]
rs4713104	0.92[ASN][1000 genomes]
rs4713105	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713106	0.88[ASN][1000 genomes]
rs4713107	0.88[ASN][1000 genomes]
rs4713109	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62401365	0.92[ASN][1000 genomes]
rs6456786	0.91[ASN][1000 genomes]
rs6456788	0.86[ASN][1000 genomes]
rs6456789	0.92[ASN][1000 genomes]
rs6650992	0.96[ASN][1000 genomes]
rs6899950	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6903282	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904844	0.97[ASN][1000 genomes]
rs6911865	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6918131	0.99[ASN][1000 genomes]
rs6918794	0.84[ASN][1000 genomes]
rs6920010	0.92[ASN][1000 genomes]
rs6920408	0.92[ASN][1000 genomes]
rs6920733	0.92[ASN][1000 genomes]
rs6921071	0.92[ASN][1000 genomes]
rs6931659	0.95[ASN][1000 genomes]
rs6933354	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs726830	0.86[ASN][1000 genomes]
rs7509	0.90[ASN][1000 genomes]
rs764460	0.92[ASN][1000 genomes]
rs764461	0.92[ASN][1000 genomes]
rs7741031	0.92[ASN][1000 genomes]
rs7743443	0.92[ASN][1000 genomes]
rs7743465	0.92[ASN][1000 genomes]
rs7744110	0.91[ASN][1000 genomes]
rs7745380	0.92[ASN][1000 genomes]
rs7748366	0.92[ASN][1000 genomes]
rs7750795	0.92[ASN][1000 genomes]
rs7754678	0.89[ASN][1000 genomes]
rs7754724	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756216	0.92[ASN][1000 genomes]
rs7756377	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7764070	0.92[ASN][1000 genomes]
rs7764634	0.88[ASN][1000 genomes]
rs7771590	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7772160	0.89[ASN][1000 genomes]
rs7774613	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7776338	0.99[ASN][1000 genomes]
rs9461386	0.86[ASN][1000 genomes]
rs9468141	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9468140	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs9468140	ZNF391	cis	lung	GTEx
rs9468140	ZNF391	cis	Artery Tibial	GTEx
rs9468140	ZNF391	cis	Heart Left Ventricle	GTEx
rs9468140	ZNF391	cis	Esophagus Muscularis	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27467800-27472000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27469400-27471600	Active TSS	K562	blood
3	chr6:27469400-27471800	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:27469400-27472000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:27469800-27471800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:27469800-27472000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:27469800-27472000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:27469800-27472000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:27470000-27471600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr6:27470000-27471600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:27470000-27471600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:27470000-27471600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr6:27470000-27471600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:27470000-27471600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:27470000-27471600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:27470000-27471600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:27470000-27471600	Active TSS	NHLF	lung
18	chr6:27470000-27471800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:27470000-27471800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr6:27470000-27471800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:27470000-27471800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:27470000-27471800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:27470000-27471800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:27470000-27472000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:27470200-27471600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:27470200-27471600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:27470200-27471600	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr6:27470200-27471600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr6:27470200-27471600	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:27470200-27471600	Active TSS	Right Atrium	heart
31	chr6:27470200-27471600	Active TSS	Right Ventricle	heart
32	chr6:27470200-27471600	Active TSS	HSMM	muscle
33	chr6:27470200-27471800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:27470200-27471800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:27470200-27471800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:27470200-27472000	Active TSS	A549	lung
37	chr6:27470400-27471600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:27470400-27471600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:27470400-27471600	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr6:27470400-27471600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:27470400-27471600	Active TSS	Brain Cingulate Gyrus	brain
42	chr6:27470400-27471600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
43	chr6:27470400-27471600	Bivalent/Poised TSS	Fetal Kidney	kidney
44	chr6:27470400-27471600	Active TSS	Ovary	ovary
45	chr6:27470400-27471600	Active TSS	Hela-S3	cervix
46	chr6:27470400-27471600	Active TSS	HSMMtube	muscle
47	chr6:27470400-27472000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
48	chr6:27470600-27471600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:27470600-27471600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:27470600-27471600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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