Variant report

Variant	rs2293390
Chromosome Location	chr6:36949527-36949528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:36946683-36950240	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:36948684-36950367	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:36949489-36950151	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:36948623-36949742	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:36948480-36949698	K562	blood:	n/a	n/a
6	POLR2A	chr6:36948990-36949538	GM12891	blood:	n/a	n/a
7	POLR2A	chr6:36948972-36949535	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36937337..36939387-chr6:36947202..36951298,3	MCF-7	breast:
2	chr6:36947258..36950041-chr6:36986048..36987573,2	MCF-7	breast:
3	chr6:36949522..36951437-chr6:36961267..36963379,2	K562	blood:
4	chr6:36949230..36952224-chr6:37136925..37139369,2	K562	blood:
5	chr6:36853647..36856578-chr6:36948651..36952350,3	K562	blood:
6	chr6:36948207..36949609-chr6:36985741..36986646,4	MCF-7	breast:
7	chr6:36939940..36941614-chr6:36949156..36950933,2	MCF-7	breast:

No data

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137193	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12524778	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs1318961	0.94[CHB][hapmap]
rs13217627	0.94[CHB][hapmap]
rs1570116	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs1753284	0.94[CHB][hapmap]
rs1753286	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs2770123	0.88[CHB][hapmap]
rs7739958	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs7743783	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs9394393	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv988069	chr6:36942299-36951067	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2293390	PI16	cis	parietal	SCAN
rs2293390	ZFAND3	cis	parietal	SCAN
rs2293390	PI16	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:36934000-36949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:36934200-36950400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:36934800-36949600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:36935000-36949800	Genic enhancers	Left Ventricle	heart
7	chr6:36935000-36950200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:36939000-36951200	Strong transcription	HSMM	muscle
9	chr6:36939400-36949600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:36939600-36950600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:36941200-36950600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:36945000-36951200	Enhancers	Fetal Heart	heart
13	chr6:36945400-36951400	Weak transcription	Fetal Kidney	kidney
14	chr6:36945600-36949800	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr6:36946200-36951000	Weak transcription	Small Intestine	intestine
16	chr6:36946200-36952000	Weak transcription	A549	lung
17	chr6:36946400-36949600	Genic enhancers	Fetal Muscle Leg	muscle
18	chr6:36946400-36949800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:36946400-36950400	Weak transcription	Ovary	ovary
20	chr6:36946400-36951200	Weak transcription	Hela-S3	cervix
21	chr6:36946400-36951600	Weak transcription	HSMMtube	muscle
22	chr6:36946400-36951800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:36946600-36949600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:36946600-36950600	Weak transcription	HUVEC	blood vessel
25	chr6:36946600-36950600	Weak transcription	NHDF-Ad	bronchial
26	chr6:36946600-36951200	Weak transcription	HMEC	breast
27	chr6:36946800-36949800	Enhancers	Brain Hippocampus Middle	brain
28	chr6:36946800-36949800	Genic enhancers	Fetal Thymus	thymus
29	chr6:36946800-36949800	Enhancers	Pancreas	Pancrea
30	chr6:36946800-36949800	Enhancers	Right Atrium	heart
31	chr6:36946800-36950600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:36946800-36950800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:36946800-36951000	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr6:36946800-36951800	Enhancers	Brain Angular Gyrus	brain
35	chr6:36946800-36951800	Genic enhancers	Brain Anterior Caudate	brain
36	chr6:36947000-36951400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:36947200-36949600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:36947200-36949800	Genic enhancers	Fetal Brain Female	brain
39	chr6:36947200-36950000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:36947200-36950000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr6:36947200-36950200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr6:36947200-36952000	Enhancers	Colon Smooth Muscle	Colon
43	chr6:36947400-36949800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr6:36947400-36949800	Genic enhancers	Fetal Stomach	stomach
45	chr6:36947400-36950800	Genic enhancers	Spleen	Spleen
46	chr6:36947400-36951200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
47	chr6:36947600-36949600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:36947600-36949800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:36947600-36950800	Strong transcription	Fetal Intestine Small	intestine
50	chr6:36947600-36951000	Weak transcription	Rectal Mucosa Donor 29	rectum

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