Variant report

Variant	rs2394250
Chromosome Location	chr6:29943656-29943657
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr6:29942686-29943660	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr6:29943179-29943683	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:29943013..29944901-chr6:29959011..29961264,2	K562	blood:
2	chr6:29933916..29936718-chr6:29943405..29945040,3	MCF-7	breast:
3	chr6:29943470..29945184-chr6:29952031..29954167,2	K562	blood:

Variant related genes	Relation type
HCG9	TF binding region
MICD	TF binding region
ENSG00000238024	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1632994	0.86[ASN][1000 genomes]
rs2428521	0.85[ASN][1000 genomes]
rs2517683	0.84[ASN][1000 genomes]
rs2517689	0.85[ASN][1000 genomes]
rs2517691	0.85[ASN][1000 genomes]
rs2517692	0.85[ASN][1000 genomes]
rs2517696	0.83[ASN][1000 genomes]
rs2523934	0.85[ASN][1000 genomes]
rs2844807	0.86[ASN][1000 genomes]
rs2904757	0.85[ASN][1000 genomes]
rs3823363	0.86[ASN][1000 genomes]
rs437289	0.85[ASN][1000 genomes]
rs441808	0.86[ASN][1000 genomes]
rs446787	0.85[ASN][1000 genomes]
rs9260721	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	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
10	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv32544	chr6:29831716-29944103	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
12	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active 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 target site	28 gene(s)	inside rSNPs	diseases
14	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
17	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv984584	chr6:29932342-29943951	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	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
23	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
24	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	esv3350882	chr6:29942373-29945471	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2394250	HLA-A	cis	lymphoblastoid	seeQTL
rs2394250	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs2394250	ZNF391	cis	cerebellum	SCAN
rs2394250	HIST1H4G	cis	cerebellum	SCAN
rs2394250	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs2394250	HIST1H2AI	cis	parietal	SCAN
rs2394250	GRM4	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29934400-29944200	Weak transcription	Aorta	Aorta
2	chr6:29935600-29944800	Weak transcription	Dnd41	blood
3	chr6:29941600-29944400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:29942600-29944200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
5	chr6:29942600-29944400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
6	chr6:29942600-29944400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr6:29942600-29944400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
8	chr6:29942600-29945200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:29942600-29945400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:29942600-29945400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:29942800-29943800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:29942800-29943800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:29942800-29943800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:29942800-29943800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
15	chr6:29942800-29944000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:29942800-29944200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr6:29942800-29944200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr6:29942800-29944400	Bivalent Enhancer	Fetal Thymus	thymus
19	chr6:29942800-29944400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr6:29942800-29944400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr6:29942800-29945400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:29943000-29943800	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
23	chr6:29943000-29944000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
24	chr6:29943000-29944000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:29943000-29944200	Bivalent Enhancer	Primary B cells from cord blood	blood
26	chr6:29943000-29944400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
27	chr6:29943000-29944400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:29943000-29944400	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr6:29943000-29944400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:29943000-29944400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr6:29943000-29944400	Flanking Active TSS	HepG2	liver
32	chr6:29943200-29943800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:29943200-29943800	Bivalent Enhancer	Fetal Brain Female	brain
34	chr6:29943200-29943800	Bivalent Enhancer	Placenta	Placenta
35	chr6:29943200-29943800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
36	chr6:29943200-29944000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:29943200-29944000	Bivalent Enhancer	GM12878-XiMat	blood
38	chr6:29943200-29944000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr6:29943200-29944200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:29943200-29944200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
41	chr6:29943200-29944400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
42	chr6:29943200-29945400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
43	chr6:29943200-29945400	Active TSS	Psoas Muscle	Psoas
44	chr6:29943400-29943800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:29943400-29943800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:29943400-29943800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:29943400-29943800	Enhancers	K562	blood
48	chr6:29943400-29943800	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
49	chr6:29943400-29944000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:29943400-29944000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon

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