Variant report

Variant	rs3095326
Chromosome Location	chr6:30725841-30725842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1049633	0.81[AMR][1000 genomes]
rs1059612	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1264308	0.81[AMR][1000 genomes]
rs1264325	0.81[AMR][1000 genomes]
rs1264347	0.81[AMR][1000 genomes]
rs1264351	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1264361	0.82[EUR][1000 genomes]
rs1264373	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2263298	0.81[AMR][1000 genomes]
rs2517578	0.81[AMR][1000 genomes]
rs2524266	0.86[EUR][1000 genomes]
rs2535328	0.81[AMR][1000 genomes]
rs2535332	0.81[AMR][1000 genomes]
rs2535334	0.81[AMR][1000 genomes]
rs2535340	0.81[AMR][1000 genomes]
rs2844656	0.81[AMR][1000 genomes]
rs3094023	0.91[AMR][1000 genomes]
rs3094024	0.81[AMR][1000 genomes]
rs3094088	0.81[AMR][1000 genomes]
rs3094118	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3094125	0.87[EUR][1000 genomes]
rs3095276	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3095327	0.81[EUR][1000 genomes]
rs3095328	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095332	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3095334	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095338	0.80[AFR][1000 genomes]
rs3129972	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3129973	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3129974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3129977	0.91[EUR][1000 genomes]
rs3129978	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3129980	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129982	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129983	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129984	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3129985	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3130117	0.91[AMR][1000 genomes]
rs3130241	0.81[AMR][1000 genomes]
rs3130247	0.91[AMR][1000 genomes]
rs3130641	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130658	0.87[EUR][1000 genomes]
rs3130660	0.87[EUR][1000 genomes]
rs3130665	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130668	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130669	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3130670	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130673	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131041	0.88[EUR][1000 genomes]
rs3131044	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131045	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131047	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131049	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131050	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131052	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3131055	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131058	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131060	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3132577	0.81[AMR][1000 genomes]
rs3132582	0.81[EUR][1000 genomes]
rs3132583	0.87[EUR][1000 genomes]
rs3132585	0.87[EUR][1000 genomes]
rs3132599	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3132603	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132605	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132610	0.82[AMR][1000 genomes]
rs886422	0.81[AMR][1000 genomes]
rs886424	0.82[EUR][1000 genomes]
rs886425	0.82[EUR][1000 genomes]
rs9262126	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262130	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262132	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262135	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9262141	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262142	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262143	0.83[EUR][1000 genomes]
rs9262146	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262174	0.80[AFR][1000 genomes]
rs9262200	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262202	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262203	0.84[AMR][1000 genomes]
rs9262204	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3095326	HLA-G	cis	multi-tissue	Pritchard
rs3095326	BTN3A2	cis	multi-tissue	Pritchard
rs3095326	HLA-DQB1	cis	multi-tissue	Pritchard
rs3095326	HLA-DRB1	cis	multi-tissue	Pritchard
rs3095326	HLA-DQA1	cis	multi-tissue	Pritchard
rs3095326	HLA-C	cis	multi-tissue	Pritchard
rs3095326	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3095326	ZFP57	cis	multi-tissue	Pritchard
rs3095326	HIST1H2BM	cis	cerebellum	SCAN
rs3095326	HLA-H	cis	multi-tissue	Pritchard
rs3095326	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30717800-30726800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:30719800-30727200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:30719800-30731600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:30720400-30731000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:30720600-30736600	Weak transcription	Gastric	stomach
6	chr6:30720800-30727000	Weak transcription	Pancreas	Pancrea
7	chr6:30720800-30727600	Weak transcription	Lung	lung
8	chr6:30720800-30727800	Weak transcription	Esophagus	oesophagus
9	chr6:30721000-30727400	Weak transcription	Aorta	Aorta
10	chr6:30721200-30726400	Weak transcription	Adipose Nuclei	Adipose
11	chr6:30721200-30726800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:30721200-30727000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:30721200-30727600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:30721400-30727400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:30721600-30726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:30721800-30726800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:30723200-30726400	Weak transcription	HSMM	muscle
18	chr6:30723400-30726600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:30723800-30726600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:30724000-30726400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:30724000-30726600	Weak transcription	HMEC	breast
22	chr6:30724000-30727000	Weak transcription	Placenta	Placenta
23	chr6:30724000-30731400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:30724200-30726400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:30724400-30726800	Enhancers	HepG2	liver
26	chr6:30724600-30727600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:30725000-30726000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:30725000-30726000	Enhancers	A549	lung
29	chr6:30725000-30726600	Enhancers	GM12878-XiMat	blood
30	chr6:30725000-30726800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:30725000-30726800	Enhancers	NHDF-Ad	bronchial
32	chr6:30725000-30728000	Enhancers	HUVEC	blood vessel
33	chr6:30725200-30727400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:30725200-30728600	Enhancers	NH-A	brain
35	chr6:30725200-30729800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:30725400-30726800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:30725400-30730000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr6:30725600-30726000	Weak transcription	Left Ventricle	heart
39	chr6:30725600-30726400	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:30725600-30726600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:30725600-30726600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:30725600-30726600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:30725600-30726600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:30725600-30726600	Weak transcription	NHEK	skin
45	chr6:30725600-30726800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:30725600-30727600	Weak transcription	Right Atrium	heart
47	chr6:30725600-30727600	Weak transcription	Spleen	Spleen
48	chr6:30725600-30731000	Weak transcription	Primary T cells from cord blood	blood
49	chr6:30725800-30726200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr6:30725800-30726200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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