Variant report

Variant	rs3094118
Chromosome Location	chr6:30732858-30732859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30731319..30733794-chr6:30880499..30882436,2	K562	blood:
2	chr6:30732229..30734221-chr6:30735941..30738002,2	K562	blood:
3	chr6:30731381..30733806-chr6:30851379..30853167,2	MCF-7	breast:
4	chr6:30731147..30732913-chr6:30849993..30851974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1059612	0.86[EUR][1000 genomes]
rs1264351	0.83[EUR][1000 genomes]
rs1264361	0.88[EUR][1000 genomes]
rs1264373	0.83[EUR][1000 genomes]
rs2524266	0.83[EUR][1000 genomes]
rs3094125	0.85[EUR][1000 genomes]
rs3095326	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3095328	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3095332	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3095334	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095338	0.93[AMR][1000 genomes]
rs3129972	0.91[EUR][1000 genomes]
rs3129973	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3129974	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3129977	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3129978	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129980	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129982	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129983	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129984	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3129985	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130641	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130658	0.85[EUR][1000 genomes]
rs3130660	0.85[EUR][1000 genomes]
rs3130665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130668	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3130669	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130670	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130673	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3131041	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131044	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131045	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131047	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131048	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131049	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131050	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131052	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3131054	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131055	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131058	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131060	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132583	0.85[EUR][1000 genomes]
rs3132585	0.85[EUR][1000 genomes]
rs3132599	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132600	0.94[EUR][1000 genomes]
rs3132603	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3132605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs886424	0.88[EUR][1000 genomes]
rs886425	0.88[EUR][1000 genomes]
rs9262126	0.83[EUR][1000 genomes]
rs9262130	0.83[EUR][1000 genomes]
rs9262132	0.83[EUR][1000 genomes]
rs9262135	0.83[EUR][1000 genomes]
rs9262141	0.80[EUR][1000 genomes]
rs9262142	0.80[EUR][1000 genomes]
rs9262143	0.80[EUR][1000 genomes]
rs9262146	0.80[EUR][1000 genomes]
rs9262174	0.93[AMR][1000 genomes]
rs9262200	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262202	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262203	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262204	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
9	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
10	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
11	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
12	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3094118	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30720600-30736600	Weak transcription	Gastric	stomach
2	chr6:30726800-30739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:30728000-30737000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:30728200-30736400	Weak transcription	Lung	lung
5	chr6:30728200-30736600	Weak transcription	Aorta	Aorta
6	chr6:30731000-30734600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30731000-30735600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:30731000-30738800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:30731200-30733000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:30731200-30734600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:30731600-30735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:30731800-30734200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:30731800-30734200	Weak transcription	Spleen	Spleen
14	chr6:30732000-30733600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:30732000-30734000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:30732000-30734000	Weak transcription	Pancreas	Pancrea
17	chr6:30732000-30734000	Weak transcription	Right Atrium	heart
18	chr6:30732000-30735200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:30732000-30735400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:30732000-30735400	Weak transcription	Thymus	Thymus
21	chr6:30732000-30736200	Weak transcription	Esophagus	oesophagus
22	chr6:30732000-30736400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:30732000-30736400	Weak transcription	Brain Anterior Caudate	brain
24	chr6:30732000-30736600	Weak transcription	HSMM	muscle
25	chr6:30732000-30736800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:30732200-30733400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:30732200-30733800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:30732200-30733800	Weak transcription	Right Ventricle	heart
29	chr6:30732200-30734200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:30732200-30734200	Weak transcription	GM12878-XiMat	blood
31	chr6:30732200-30734400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:30732200-30734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:30732200-30734800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:30732200-30735400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:30732200-30735600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:30732200-30736200	Weak transcription	NHLF	lung
37	chr6:30732200-30736400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:30732200-30736400	Weak transcription	NHDF-Ad	bronchial
39	chr6:30732200-30736600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:30732200-30736800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:30732200-30737000	Weak transcription	Fetal Lung	lung
42	chr6:30732400-30733200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr6:30732400-30733200	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr6:30732400-30733400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:30732400-30733800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:30732400-30734000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:30732400-30734000	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:30732400-30734000	Weak transcription	Left Ventricle	heart
49	chr6:30732400-30734000	Weak transcription	Stomach Mucosa	stomach
50	chr6:30732400-30734000	Weak transcription	Stomach Smooth Muscle	stomach

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