Variant report

Variant	rs7743465
Chromosome Location	chr6:27426717-27426718
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27283533..27286469-chr6:27424537..27427357,2	K562	blood:
2	chr6:27414915..27419456-chr6:27425103..27430538,5	MCF-7	breast:
3	chr6:27424492..27429899-chr6:27438525..27441854,6	K562	blood:
4	chr6:27426287..27427863-chr6:27440014..27442543,2	MCF-7	breast:
5	chr6:27426149..27428000-chr6:27437055..27440025,2	K562	blood:

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1014227	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10452601	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10484396	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10484397	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10484398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807023	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10807024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807025	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10946917	0.84[EUR][1000 genomes]
rs10946918	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10946919	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946921	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10946931	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10946932	0.92[ASN][1000 genomes]
rs10946933	0.91[ASN][1000 genomes]
rs11970336	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12197858	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12199110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12200018	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12205189	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12206045	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12212288	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12212293	0.84[ASN][1000 genomes]
rs12213598	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12215117	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12524409	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12525255	0.84[EUR][1000 genomes]
rs12525544	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12528904	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12529839	0.99[ASN][1000 genomes]
rs12529840	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13201443	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13201965	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13201985	0.99[ASN][1000 genomes]
rs13207099	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13212050	0.92[ASN][1000 genomes]
rs13215560	0.92[ASN][1000 genomes]
rs13217162	0.92[ASN][1000 genomes]
rs13217248	0.92[ASN][1000 genomes]
rs13217798	0.82[ASN][1000 genomes]
rs13220155	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1569566	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1883216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049944	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2049945	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2092120	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2092121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103557	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2142705	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2179154	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2205831	0.83[ASN][1000 genomes]
rs2206253	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2206254	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2235252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272814	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2272815	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2272816	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2294308	0.92[ASN][1000 genomes]
rs2294309	0.91[ASN][1000 genomes]
rs2893916	0.83[ASN][1000 genomes]
rs2893917	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34185469	0.82[ASN][1000 genomes]
rs35394453	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3918438	0.87[EUR][1000 genomes]
rs4478400	0.90[ASN][1000 genomes]
rs4711150	0.82[EUR][1000 genomes]
rs4711151	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711153	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713096	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4713097	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4713101	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713104	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713105	0.99[ASN][1000 genomes]
rs4713106	0.95[ASN][1000 genomes]
rs4713107	0.95[ASN][1000 genomes]
rs4713109	0.92[ASN][1000 genomes]
rs55705181	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57647048	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62401131	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62401133	0.81[EUR][1000 genomes]
rs62401365	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6456784	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6456785	0.82[ASN][1000 genomes]
rs6456786	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6456788	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6456789	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456791	0.85[ASN][1000 genomes]
rs6650992	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6899780	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6899950	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6900278	0.84[EUR][1000 genomes]
rs6903282	0.90[ASN][1000 genomes]
rs6904844	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6908086	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6911865	0.92[ASN][1000 genomes]
rs6914542	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6914585	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918131	0.91[ASN][1000 genomes]
rs6918794	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6920010	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6920408	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6920733	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6921071	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6926142	0.83[ASN][1000 genomes]
rs6928314	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6929812	0.82[ASN][1000 genomes]
rs6931659	0.88[ASN][1000 genomes]
rs6933354	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6938943	0.84[EUR][1000 genomes]
rs726830	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7509	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs760880	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs764460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741031	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7743443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744110	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745380	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7747283	0.84[ASN][1000 genomes]
rs7747444	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7748366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750795	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7754086	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7754678	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7754724	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7754977	0.82[ASN][1000 genomes]
rs7756216	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7756377	0.92[ASN][1000 genomes]
rs7764070	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7764634	0.95[ASN][1000 genomes]
rs7771590	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7771598	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7772160	0.96[ASN][1000 genomes]
rs7774613	0.90[ASN][1000 genomes]
rs7776338	0.91[ASN][1000 genomes]
rs9468134	0.85[AFR][1000 genomes]
rs9468140	0.92[ASN][1000 genomes]
rs9468141	0.92[ASN][1000 genomes]
rs979352	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs979353	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][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	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
2	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
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7743465	ZNF391	cis	lung	GTEx
rs7743465	ZNF391	cis	Nerve Tibial	GTEx
rs7743465	ZNF391	cis	Artery Tibial	GTEx
rs7743465	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs7743465	ZNF391	cis	Esophagus Muscularis	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27412600-27438000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:27414200-27430600	ZNF genes & repeats	Liver	Liver
3	chr6:27414400-27432000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
4	chr6:27415400-27430000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:27415400-27438600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:27415600-27427400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
7	chr6:27415600-27429800	ZNF genes & repeats	Dnd41	blood
8	chr6:27415600-27430000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:27415600-27430000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:27415600-27430200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr6:27415800-27430000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:27415800-27430200	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr6:27415800-27434000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr6:27416000-27432400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:27416200-27432600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:27416400-27428000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr6:27416600-27429200	ZNF genes & repeats	HSMM	muscle
18	chr6:27416800-27429400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
19	chr6:27416800-27430600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
20	chr6:27417200-27432600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:27417400-27427400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
22	chr6:27417600-27427000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr6:27417600-27430000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
24	chr6:27417800-27429400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
25	chr6:27418000-27430200	ZNF genes & repeats	GM12878-XiMat	blood
26	chr6:27422800-27428200	Weak transcription	Stomach Mucosa	stomach
27	chr6:27422800-27429000	Strong transcription	Brain Hippocampus Middle	brain
28	chr6:27422800-27430000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:27422800-27430400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:27423000-27430200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:27424000-27439800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:27424800-27427600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:27424800-27427600	Weak transcription	Esophagus	oesophagus
34	chr6:27424800-27427600	Weak transcription	Lung	lung
35	chr6:27424800-27427600	Weak transcription	Pancreas	Pancrea
36	chr6:27425000-27438800	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:27425200-27426800	Weak transcription	Left Ventricle	heart
38	chr6:27425200-27426800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:27425200-27426800	Weak transcription	Thymus	Thymus
40	chr6:27425200-27427400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:27425200-27427600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:27425200-27427600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:27425200-27427600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr6:27425200-27427600	Weak transcription	Fetal Stomach	stomach
45	chr6:27425200-27427600	Weak transcription	Gastric	stomach
46	chr6:27425200-27428200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:27425200-27428600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:27425200-27428600	Weak transcription	Spleen	Spleen
49	chr6:27425200-27429400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:27425200-27433800	Weak transcription	Psoas Muscle	Psoas

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