Variant report

Variant	rs7549545
Chromosome Location	chr1:180939058-180939059
allele	C/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	BCL3	chr1:180939011-180939365	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:180938921-180939246	GM12878	blood:	n/a	n/a
3	SPI1	chr1:180938356-180939092	GM12878	blood:	n/a	chr1:180938875-180938884 chr1:180938869-180938882
4	POLR2A	chr1:180939008-180939231	GM12891	blood:	n/a	n/a
5	PBX3	chr1:180939011-180939263	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:180938469-180939226	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:180938387-180939318	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:180938380-180939269	GM12892	blood:	n/a	n/a
9	SPI1	chr1:180938606-180939075	GM12891	blood:	n/a	chr1:180938875-180938884 chr1:180938869-180938882
10	BATF	chr1:180938982-180939248	GM12878	blood:	n/a	n/a
11	EBF1	chr1:180938436-180939273	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180938779..180940464-chr1:181056707..181058970,2	K562	blood:
2	chr1:180938068..180941019-chr1:181056460..181059037,4	K562	blood:
3	chr1:180932996..180935455-chr1:180937795..180941673,3	MCF-7	breast:
4	chr1:180933034..180938105-chr1:180938834..180942220,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234237	TF binding region
ENSG00000270711	TF binding region
ENSG00000162783	Chromatin interaction
ENSG00000251520	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10914143	0.95[CHB][hapmap];0.94[GIH][hapmap]
rs12022368	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap]

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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7549545	RGS8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180918600-180939800	Weak transcription	K562	blood
3	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:180922600-180949400	Strong transcription	Dnd41	blood
5	chr1:180923600-180944800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
7	chr1:180923800-180942800	Weak transcription	Fetal Lung	lung
8	chr1:180923800-180944800	Weak transcription	HUVEC	blood vessel
9	chr1:180923800-180944800	Weak transcription	NH-A	brain
10	chr1:180924000-180939200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:180924000-180939400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:180924000-180940000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:180924000-180940200	Weak transcription	Gastric	stomach
14	chr1:180924000-180941600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:180924200-180940000	Weak transcription	NHDF-Ad	bronchial
16	chr1:180924200-180941600	Weak transcription	Pancreas	Pancrea
17	chr1:180924200-180942000	Weak transcription	Liver	Liver
18	chr1:180924200-180943400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:180929000-180956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:180929600-180939200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:180930200-180939600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:180930200-180950200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:180930800-180939200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:180931200-180939600	Weak transcription	HSMM	muscle
25	chr1:180931400-180939200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:180931600-180941800	Weak transcription	Placenta	Placenta
27	chr1:180931600-180950800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:180932000-180940200	Weak transcription	Ovary	ovary
29	chr1:180932000-180942600	Weak transcription	HSMMtube	muscle
30	chr1:180932000-180944800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:180932200-180941600	Weak transcription	Fetal Kidney	kidney
32	chr1:180932200-180942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:180932800-180943000	Strong transcription	Fetal Stomach	stomach
34	chr1:180933200-180947200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:180933400-180948000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:180933600-180943400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:180933800-180944200	Strong transcription	Primary T cells from cord blood	blood
39	chr1:180933800-180948800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:180934200-180943800	Strong transcription	Fetal Intestine Large	intestine
41	chr1:180934800-180940200	Weak transcription	Fetal Brain Female	brain
42	chr1:180935600-180939200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:180935600-180939400	Enhancers	Psoas Muscle	Psoas
44	chr1:180935600-180940600	Genic enhancers	Fetal Muscle Leg	muscle
45	chr1:180936000-180939800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:180936200-180939200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:180936200-180939400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:180936200-180940200	Weak transcription	Osteobl	bone
49	chr1:180936400-180939200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:180936400-180941600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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