Variant report

Variant	rs13194003
Chromosome Location	chr6:88357749-88357750
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88298172..88299794-chr6:88356320..88357949,2	K562	blood:
2	chr6:88355100..88357756-chr6:88404547..88407101,2	K562	blood:

Variant related genes	Relation type
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10755484	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13193380	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246113	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2307379	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2325064	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2754247	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2754248	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2754260	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2754262	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2787893	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2787921	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2787924	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814712	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3757368	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3934838	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4334949	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4464759	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4498321	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4587138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587143	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4706294	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707373	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707374	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4707376	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707377	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707379	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707382	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707383	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6454631	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454632	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454636	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454638	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454640	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454641	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6906769	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6908386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916732	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6918909	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6928160	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6930600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6931069	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940150	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7741825	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742965	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7746465	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7750207	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7752494	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7755167	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757636	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7757794	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7762864	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7772561	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7773906	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444512	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444519	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444522	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444524	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9444525	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444526	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444530	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450723	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450732	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450733	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450738	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450739	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450744	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450752	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450755	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450762	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13194003	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs13194003	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs13194003	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:88308800-88369800	Weak transcription	Fetal Brain Male	brain
5	chr6:88312200-88371200	Weak transcription	NHEK	skin
6	chr6:88312400-88380600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
8	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
10	chr6:88316600-88381200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
12	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:88323000-88366400	Weak transcription	A549	lung
15	chr6:88324000-88369800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:88324000-88385000	Weak transcription	Gastric	stomach
17	chr6:88324200-88366600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:88324200-88369000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:88324200-88370200	Weak transcription	Psoas Muscle	Psoas
20	chr6:88324200-88378200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:88324200-88380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:88325400-88369200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:88327200-88362000	Weak transcription	Fetal Heart	heart
24	chr6:88329800-88383200	Weak transcription	Lung	lung
25	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
26	chr6:88334600-88362600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:88338800-88369600	Weak transcription	HSMMtube	muscle
28	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
29	chr6:88340000-88370000	Weak transcription	Spleen	Spleen
30	chr6:88340200-88364400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:88340600-88364400	Weak transcription	NHLF	lung
32	chr6:88340600-88368400	Weak transcription	NHDF-Ad	bronchial
33	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:88346400-88369600	Weak transcription	NH-A	brain
35	chr6:88346600-88362200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:88346600-88362800	Weak transcription	HMEC	breast
37	chr6:88346600-88363600	Weak transcription	Left Ventricle	heart
38	chr6:88346600-88366600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:88346600-88373800	Weak transcription	Fetal Kidney	kidney
40	chr6:88346600-88376400	Weak transcription	Brain Hippocampus Middle	brain
41	chr6:88347000-88366600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:88347800-88363000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:88347800-88369200	Weak transcription	HSMM	muscle
44	chr6:88347800-88378000	Weak transcription	Fetal Brain Female	brain
45	chr6:88348000-88367000	Weak transcription	Osteobl	bone
46	chr6:88348000-88369200	Weak transcription	Aorta	Aorta
47	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:88348600-88377600	Weak transcription	Brain Anterior Caudate	brain
49	chr6:88349000-88362200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:88349000-88362200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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