Variant report

Variant	rs4774612
Chromosome Location	chr15:52511465-52511466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1077383	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11855672	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.86[ASN][1000 genomes]
rs12593936	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs12593939	0.84[ASN][1000 genomes]
rs12595160	1.00[ASW][hapmap];0.89[GIH][hapmap]
rs12903539	0.86[ASN][1000 genomes]
rs12916135	0.80[ASN][1000 genomes]
rs34276836	0.93[ASN][1000 genomes]
rs35712143	0.84[ASN][1000 genomes]
rs4776010	1.00[CHB][hapmap];0.89[GIH][hapmap];0.82[ASN][1000 genomes]
rs4776011	0.82[ASN][1000 genomes]
rs4776013	0.82[ASN][1000 genomes]
rs4776014	0.82[ASN][1000 genomes]
rs66566761	0.84[ASN][1000 genomes]
rs67163040	0.84[ASN][1000 genomes]
rs67447954	0.91[ASN][1000 genomes]
rs71472930	1.00[ASN][1000 genomes]
rs7164508	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7172037	0.84[ASN][1000 genomes]
rs7183278	0.82[ASN][1000 genomes]
rs8025737	1.00[CHB][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4774612	BCL2L10	cis	parietal	SCAN
rs4774612	PSTPIP2	trans	lymphoblastoid	seeQTL
rs4774612	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs4774612	BCL2L10	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:52495600-52519000	Strong transcription	HepG2	liver
7	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
11	chr15:52499200-52512600	Strong transcription	A549	lung
12	chr15:52500000-52512000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr15:52501400-52512400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr15:52501600-52519000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
18	chr15:52502000-52519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:52502000-52523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:52502400-52520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:52502600-52519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:52502800-52517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:52503200-52512400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr15:52503200-52519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:52504400-52512600	Weak transcription	Placenta	Placenta
26	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
27	chr15:52505600-52525600	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:52505800-52513000	Weak transcription	Primary T cells from cord blood	blood
30	chr15:52506000-52516400	Weak transcription	Spleen	Spleen
31	chr15:52506200-52512600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:52506400-52514600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
34	chr15:52508200-52513000	Strong transcription	Fetal Intestine Small	intestine
35	chr15:52508600-52518800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr15:52508600-52519000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:52508800-52511600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:52509000-52511800	Strong transcription	Esophagus	oesophagus
39	chr15:52509000-52511800	Strong transcription	Gastric	stomach
40	chr15:52509000-52511800	Strong transcription	Pancreas	Pancrea
41	chr15:52509000-52512000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:52509000-52512400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:52509000-52512600	Strong transcription	Fetal Intestine Large	intestine
44	chr15:52509000-52512800	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr15:52509000-52512800	Strong transcription	Colonic Mucosa	Colon
46	chr15:52509000-52516000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:52509000-52516400	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:52509000-52516400	Strong transcription	Fetal Stomach	stomach
49	chr15:52509000-52519000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:52509000-52519000	Strong transcription	Duodenum Mucosa	Duodenum

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