Variant report

Variant	rs3778027
Chromosome Location	chr6:36939213-36939214
allele	A/G
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	POLR2A	chr6:36939201-36940260	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:36938159-36939831	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:36939133-36939599	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:36937738-36939950	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:36937680-36939988	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:36939129-36939804	GM12891	blood:	n/a	n/a
7	POLR2A	chr6:36933825-36941021	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:36939107-36939266	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36938832..36941814-chr6:36942476..36945654,4	MCF-7	breast:
2	chr6:36934908..36939247-chr6:36952489..36955593,6	MCF-7	breast:

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4714025	0.81[GIH][hapmap]
rs707998	0.81[GIH][hapmap]
rs831506	0.81[LWK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3778027	TSPO2	cis	cerebellum	SCAN
rs3778027	LRFN2	cis	parietal	SCAN
rs3778027	HMGA1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36931800-36948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36932400-36946800	Strong transcription	Fetal Brain Female	brain
3	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:36932800-36947400	Strong transcription	Fetal Stomach	stomach
5	chr6:36933800-36940400	Strong transcription	Adipose Nuclei	Adipose
6	chr6:36933800-36946800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:36933800-36946800	Strong transcription	Brain Anterior Caudate	brain
8	chr6:36933800-36947200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:36934000-36940600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:36934000-36941000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:36934000-36946600	Strong transcription	Thymus	Thymus
12	chr6:36934000-36946800	Strong transcription	Primary T cells from cord blood	blood
13	chr6:36934000-36946800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:36934000-36946800	Strong transcription	Colon Smooth Muscle	Colon
15	chr6:36934000-36949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:36934200-36940800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr6:36934200-36941000	Strong transcription	Brain Hippocampus Middle	brain
19	chr6:36934200-36946600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:36934200-36946600	Strong transcription	NHDF-Ad	bronchial
21	chr6:36934200-36946800	Strong transcription	Brain Germinal Matrix	brain
22	chr6:36934200-36947000	Strong transcription	Osteobl	bone
23	chr6:36934200-36947200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:36934200-36947400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:36934200-36949200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:36934200-36950400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:36934400-36943000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:36934400-36946000	Strong transcription	Primary B cells from cord blood	blood
29	chr6:36934400-36946400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:36934400-36946600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:36934400-36946600	Strong transcription	Aorta	Aorta
32	chr6:36934400-36946600	Strong transcription	Brain Cingulate Gyrus	brain
33	chr6:36934400-36946600	Strong transcription	Colonic Mucosa	Colon
34	chr6:36934400-36947200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:36934400-36947200	Strong transcription	NHLF	lung
36	chr6:36934400-36947400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr6:36934400-36947800	Strong transcription	Dnd41	blood
38	chr6:36934400-36949200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:36934600-36947200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:36934600-36947400	Strong transcription	NH-A	brain
41	chr6:36934600-36947600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:36934600-36949200	Strong transcription	Placenta	Placenta
43	chr6:36934800-36940600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:36934800-36940800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:36934800-36945400	Strong transcription	Brain Angular Gyrus	brain
46	chr6:36934800-36946800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:36934800-36947000	Strong transcription	Liver	Liver
48	chr6:36934800-36949600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr6:36935000-36940000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:36935000-36940600	Strong transcription	Brain Substantia Nigra	brain

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