Variant report

Variant	rs3095340
Chromosome Location	chr6:30726939-30726940
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30726903..30729816-chr6:30736090..30739671,3	K562	blood:
2	chr6:30725912..30728357-chr6:30744418..30747133,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11963870	0.94[ASN][1000 genomes]
rs11964556	0.94[ASN][1000 genomes]
rs11964596	0.94[ASN][1000 genomes]
rs11966040	0.94[ASN][1000 genomes]
rs35278546	0.94[ASN][1000 genomes]
rs35826335	0.94[ASN][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3095340	HLA-DRB1	cis	multi-tissue	Pritchard
rs3095340	BTN3A2	cis	multi-tissue	Pritchard
rs3095340	VARSL	cis	multi-tissue	Pritchard
rs3095340	HLA-A	cis	multi-tissue	Pritchard
rs3095340	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3095340	IER3	cis	lymphoblastoid	seeQTL
rs3095340	HLA-DQA1	cis	multi-tissue	Pritchard
rs3095340	HLA-H	cis	multi-tissue	Pritchard
rs3095340	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30719800-30727200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:30719800-30731600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:30720400-30731000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:30720600-30736600	Weak transcription	Gastric	stomach
5	chr6:30720800-30727000	Weak transcription	Pancreas	Pancrea
6	chr6:30720800-30727600	Weak transcription	Lung	lung
7	chr6:30720800-30727800	Weak transcription	Esophagus	oesophagus
8	chr6:30721000-30727400	Weak transcription	Aorta	Aorta
9	chr6:30721200-30727000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:30721200-30727600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:30721400-30727400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:30724000-30727000	Weak transcription	Placenta	Placenta
13	chr6:30724000-30731400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:30724600-30727600	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:30725000-30728000	Enhancers	HUVEC	blood vessel
16	chr6:30725200-30727400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:30725200-30728600	Enhancers	NH-A	brain
18	chr6:30725200-30729800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:30725400-30730000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr6:30725600-30727600	Weak transcription	Right Atrium	heart
21	chr6:30725600-30727600	Weak transcription	Spleen	Spleen
22	chr6:30725600-30731000	Weak transcription	Primary T cells from cord blood	blood
23	chr6:30725800-30727000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:30725800-30727600	Weak transcription	Right Ventricle	heart
25	chr6:30726000-30728200	Enhancers	Left Ventricle	heart
26	chr6:30726200-30728200	Enhancers	NHLF	lung
27	chr6:30726200-30729800	Enhancers	HSMMtube	muscle
28	chr6:30726200-30730000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:30726400-30727800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:30726400-30728000	Enhancers	Adipose Nuclei	Adipose
31	chr6:30726400-30728200	Enhancers	HSMM	muscle
32	chr6:30726400-30729200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:30726400-30730200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:30726600-30727000	Enhancers	Primary B cells from cord blood	blood
35	chr6:30726600-30727000	Flanking Active TSS	GM12878-XiMat	blood
36	chr6:30726600-30727200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr6:30726600-30727200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:30726600-30727200	Enhancers	Fetal Intestine Large	intestine
39	chr6:30726600-30727200	Flanking Active TSS	A549	lung
40	chr6:30726600-30727400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:30726600-30727400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:30726600-30727400	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:30726600-30727800	Enhancers	Fetal Intestine Small	intestine
44	chr6:30726600-30727800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:30726600-30728000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:30726600-30728000	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:30726600-30728000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr6:30726600-30728200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:30726600-30728200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:30726600-30728200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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