Variant report

Variant	rs7769789
Chromosome Location	chr6:109771955-109771956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109769023-109772168	GM19099	blood:	n/a	n/a
2	POLR2A	chr6:109771944-109772425	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:109766660-109772354	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:109767219-109772309	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:109767216-109772257	GM18505	blood:	n/a	n/a
6	POLR2A	chr6:109767128-109772358	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:109767429-109772368	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr6:109767133-109771962	K562	blood:	n/a	n/a
9	NFIC	chr6:109771876-109772411	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr6:109771918-109772001	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:109761500-109772072	GM12892	blood:	n/a	n/a
12	NFIC	chr6:109771951-109772402	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr6:109766420-109772338	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:109761656-109772338	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:109761808-109772355	GM12891	blood:	n/a	n/a
16	POLR2A	chr6:109763255-109772269	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:48610607..48612431-chr6:109769391..109772188,2	MCF-7	breast:
2	chr6:109770371..109773024-chr6:109807786..109809712,3	MCF-7	breast:

No data

Variant related genes	Relation type
MICAL1	TF binding region
ENSG00000223537	Chromatin interaction
ENSG00000049283	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1146240	1.00[ASW][hapmap]
rs1925921	1.00[CHB][hapmap]
rs6568576	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6568583	1.00[CHB][hapmap]
rs6912368	1.00[CHB][hapmap]
rs6921303	1.00[CHB][hapmap]
rs6931630	1.00[CHB][hapmap]
rs6937229	1.00[ASW][hapmap]
rs7775420	1.00[CHB][hapmap]
rs9372220	1.00[CHB][hapmap]
rs9400289	1.00[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7769789	FIG4	cis	cerebellum	SCAN
rs7769789	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763200-109774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
4	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
5	chr6:109763400-109775000	Strong transcription	NHLF	lung
6	chr6:109763400-109775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:109763600-109773200	Weak transcription	Fetal Brain Male	brain
8	chr6:109763600-109775000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:109763600-109775200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:109763600-109775800	Weak transcription	Right Atrium	heart
11	chr6:109763800-109774400	Strong transcription	HSMM	muscle
12	chr6:109763800-109774600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:109763800-109774800	Strong transcription	Fetal Stomach	stomach
14	chr6:109763800-109774800	Weak transcription	Small Intestine	intestine
15	chr6:109763800-109775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:109763800-109775400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:109763800-109775600	Weak transcription	HepG2	liver
18	chr6:109764000-109774400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr6:109764000-109774600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr6:109764000-109774800	Strong transcription	Fetal Intestine Large	intestine
21	chr6:109764000-109775000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:109764200-109774600	Strong transcription	Brain Germinal Matrix	brain
23	chr6:109764200-109774600	Weak transcription	Stomach Mucosa	stomach
24	chr6:109764200-109774800	Strong transcription	Fetal Brain Female	brain
25	chr6:109764400-109775800	Weak transcription	Hela-S3	cervix
26	chr6:109765400-109773600	Strong transcription	NHDF-Ad	bronchial
27	chr6:109765400-109773800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:109766600-109775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:109766800-109773200	Weak transcription	NH-A	brain
30	chr6:109766800-109775200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:109767000-109775600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:109767000-109776000	Weak transcription	A549	lung
33	chr6:109767200-109776000	Weak transcription	Osteobl	bone
34	chr6:109767400-109774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:109767800-109773000	Weak transcription	HMEC	breast
36	chr6:109768000-109772200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:109768000-109772800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:109768200-109772600	Weak transcription	Fetal Lung	lung
39	chr6:109768200-109772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:109768200-109774800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:109768400-109772000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:109768400-109772800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:109768400-109772800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:109768400-109773000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:109768400-109775800	Weak transcription	Liver	Liver
46	chr6:109768400-109775800	Weak transcription	Left Ventricle	heart
47	chr6:109768400-109776000	Weak transcription	Ovary	ovary
48	chr6:109768400-109776400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:109768400-109776400	Weak transcription	K562	blood
50	chr6:109768600-109772000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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