Variant report

Variant	rs8042947
Chromosome Location	chr15:40325860-40325861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40325553..40329490-chr15:40330087..40333048,4	MCF-7	breast:
2	chr15:40318814..40321249-chr15:40324254..40326485,2	K562	blood:
3	chr15:40317457..40319484-chr15:40324192..40326338,2	K562	blood:

Variant related genes	Relation type
ENSG00000140319	Chromatin interaction
ENSG00000248508	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12441342	0.87[ASN][1000 genomes]
rs2291622	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2898985	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3986354	0.95[JPT][hapmap]
rs4432245	0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4594236	0.83[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs711906	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs8042947	BMI1	cis	Liver	GTEx
rs8042947	FOXL1	cis	Liver	GTEx
rs8042947	hCT2281198	cis	multi-tissue	Pritchard
rs8042947	SRP14-AS1	cis	Muscle Skeletal	GTEx
rs8042947	FOXL1	trans	multi-tissue	Pritchard
rs8042947	EIF2AK4	cis	cerebellum	SCAN
rs8042947	MYST2	cis	Liver	GTEx
rs8042947	KREMEN1	trans	multi-tissue	Pritchard
rs8042947	SRP14-AS1	cis	lung	GTEx
rs8042947	BC041482	cis	multi-tissue	Pritchard
rs8042947	GH2	trans	multi-tissue	Pritchard
rs8042947	BMI1	trans	multi-tissue	Pritchard
rs8042947	SRP14	cis	Liver	GTEx
rs8042947	SRP14	cis	parietal	SCAN
rs8042947	KREMEN1	cis	Liver	GTEx
rs8042947	XM_121736	trans	multi-tissue	Pritchard
rs8042947	GH2	cis	Liver	GTEx
rs8042947	VPS18	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40303000-40329600	Strong transcription	Liver	Liver
2	chr15:40305200-40330200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:40306800-40328800	Weak transcription	Stomach Mucosa	stomach
4	chr15:40306800-40329800	Strong transcription	Osteobl	bone
5	chr15:40307000-40329000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:40307000-40329400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:40307200-40329600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:40307400-40326800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:40307400-40329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:40307600-40326200	Strong transcription	HSMM	muscle
11	chr15:40307600-40329200	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr15:40307600-40329200	Strong transcription	HMEC	breast
13	chr15:40307800-40329600	Strong transcription	NH-A	brain
14	chr15:40307800-40330000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:40308000-40329000	Strong transcription	HepG2	liver
16	chr15:40308000-40329600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:40308000-40329800	Strong transcription	NHDF-Ad	bronchial
18	chr15:40308000-40330000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr15:40308200-40329600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:40308600-40328800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:40308600-40330000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:40308800-40330000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:40309200-40329600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:40310000-40326400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr15:40310000-40329200	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:40310000-40329400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:40310000-40330000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr15:40310600-40328800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:40310600-40329800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:40310600-40330000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:40310600-40330000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr15:40313600-40329200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:40313600-40329800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:40313800-40326200	Weak transcription	Small Intestine	intestine
35	chr15:40314000-40329600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:40314000-40330400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:40315000-40328400	Weak transcription	Aorta	Aorta
38	chr15:40315000-40329600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:40315000-40329800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:40315000-40330000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:40316400-40329200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:40316400-40329400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:40316400-40330200	Strong transcription	Placenta	Placenta
44	chr15:40316800-40329800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:40317800-40329400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:40318000-40326400	Weak transcription	Esophagus	oesophagus
47	chr15:40318400-40326400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:40318400-40327000	Weak transcription	Psoas Muscle	Psoas
49	chr15:40319200-40330000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:40319800-40329800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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