Variant report

Variant	rs3094024
Chromosome Location	chr6:30495860-30495861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30456435..30458673-chr6:30494431..30497074,2	MCF-7	breast:
2	chr6:30455644..30457462-chr6:30495249..30496782,2	K562	blood:
3	chr6:30495618..30498442-chr6:30501086..30503678,2	MCF-7	breast:
4	chr6:30494697..30497060-chr6:30502191..30504973,2	K562	blood:
5	chr6:30494651..30496200-chr6:30498206..30500229,2	K562	blood:

Variant related genes	Relation type
ENSG00000204592	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1059612	0.90[AMR][1000 genomes]
rs3094023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095276	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095326	0.81[AMR][1000 genomes]
rs3095328	0.81[AMR][1000 genomes]
rs3095332	0.81[AMR][1000 genomes]
rs3129973	0.81[AMR][1000 genomes]
rs3129974	0.81[AMR][1000 genomes]
rs3130117	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130247	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131112	0.86[EUR][1000 genomes]
rs3132610	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132616	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9262126	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262130	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262132	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262135	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9262141	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262142	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262143	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262146	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	nsv884077	chr6:30434900-30512163	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
7	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3094024	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30486000-30500000	Weak transcription	Thymus	Thymus
2	chr6:30494800-30496600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:30495000-30498800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:30495000-30499000	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:30495000-30501200	Enhancers	Primary B cells from cord blood	blood
6	chr6:30495200-30496000	Active TSS	Duodenum Mucosa	Duodenum
7	chr6:30495200-30496000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr6:30495200-30496200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:30495200-30498400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:30495200-30498400	Enhancers	Fetal Intestine Large	intestine
11	chr6:30495200-30498600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:30495200-30498600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:30495200-30498600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:30495200-30498800	Enhancers	HepG2	liver
15	chr6:30495400-30496200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:30495400-30496200	Enhancers	HSMMtube	muscle
17	chr6:30495400-30496400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:30495400-30496400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:30495400-30496400	Enhancers	Fetal Intestine Small	intestine
20	chr6:30495400-30496400	Enhancers	HMEC	breast
21	chr6:30495400-30498000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr6:30495400-30498400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:30495400-30498600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:30495400-30498800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:30495400-30499000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:30495600-30496000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr6:30495600-30496200	Weak transcription	Stomach Mucosa	stomach
28	chr6:30495600-30498200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:30495600-30498400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:30495800-30496000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr6:30495800-30496000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:30495800-30496000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:30495800-30496000	Flanking Active TSS	Fetal Stomach	stomach
34	chr6:30495800-30496000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr6:30495800-30496000	Enhancers	Right Atrium	heart
36	chr6:30495800-30496000	Active TSS	NHDF-Ad	bronchial
37	chr6:30495800-30496200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:30495800-30496200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:30495800-30496200	Enhancers	Primary hematopoietic stem cells	blood
40	chr6:30495800-30496200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:30495800-30496200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:30495800-30496200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:30495800-30496200	Enhancers	Colon Smooth Muscle	Colon
44	chr6:30495800-30496200	Flanking Active TSS	A549	lung
45	chr6:30495800-30496200	Flanking Active TSS	Hela-S3	cervix
46	chr6:30495800-30496200	Enhancers	HSMM	muscle
47	chr6:30495800-30496200	Flanking Active TSS	HUVEC	blood vessel
48	chr6:30495800-30496200	Enhancers	K562	blood
49	chr6:30495800-30496200	Flanking Active TSS	NH-A	brain
50	chr6:30495800-30496200	Flanking Active TSS	NHEK	skin

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