Variant report

Variant	rs3121594
Chromosome Location	chr6:30002441-30002442
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29999651..30002590-chr6:30017205..30019223,2	K562	blood:
2	chr6:30001672..30004034-chr6:30026395..30027961,2	K562	blood:
3	chr6:30002424..30006428-chr6:30027567..30030890,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs166327	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2240619	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2394255	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3094144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098018	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3115635	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132682	0.85[ASN][1000 genomes]
rs3869065	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3869070	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3873293	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3891158	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6457120	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6457121	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6457126	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923777	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261006	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261244	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261301	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv884045	chr6:29997312-30015905	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv884046	chr6:29997312-30023868	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv884047	chr6:29998872-30007493	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3121594	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29976600-30023000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:29977200-30003800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
9	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:29979600-30022800	Weak transcription	Ovary	ovary
12	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
13	chr6:29980200-30012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:29981200-30023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:29981800-30010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:29982800-30009800	Weak transcription	Psoas Muscle	Psoas
17	chr6:29982800-30022800	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:29983400-30012400	Weak transcription	NHEK	skin
19	chr6:29984600-30023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:29985000-30024600	Weak transcription	Brain Angular Gyrus	brain
21	chr6:29985400-30008200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:29987800-30010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
24	chr6:29988000-30010400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:29988200-30009800	Weak transcription	HepG2	liver
26	chr6:29988200-30022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
29	chr6:29988400-30006200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:29988400-30021600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:29988400-30023400	Weak transcription	Adipose Nuclei	Adipose
32	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
33	chr6:29988600-30003800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:29988600-30009800	Weak transcription	Left Ventricle	heart
35	chr6:29988600-30022200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:29988800-30022800	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:29989000-30009800	Weak transcription	GM12878-XiMat	blood
39	chr6:29989000-30023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:29989400-30021400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:29989800-30003600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:29996600-30012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:29998400-30012200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:29998400-30012200	Weak transcription	HMEC	breast
46	chr6:29999000-30002600	Weak transcription	Lung	lung
47	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
48	chr6:29999800-30012400	Weak transcription	Hela-S3	cervix
49	chr6:29999800-30022200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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