Variant report

Variant	rs6496897
Chromosome Location	chr15:92692245-92692246
allele	C/T
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	POLR2A	chr15:92692229-92692620	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr15:92692085-92692621	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr15:92692239-92692560	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr15:92692204-92692594	SH-SY5Y	brain:	n/a	n/a
5	TCF12	chr15:92692078-92692830	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr15:92692100-92692847	SK-N-SH	brain:	n/a	n/a
7	EP300	chr15:92692225-92692616	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr15:92692240-92692390	BJ	skin:	n/a	n/a
9	CTCF	chr15:92692220-92692370	AG09309	skin:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM174B-5	chr15:92691981-92693013	ENSG00000249094
2	lnc-FAM174B-5	chr15:92691982-92693013	ENSG00000260661.1

Variant related genes	Relation type
SLCO3A1	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2215084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238350	0.84[EUR][1000 genomes]
rs2238358	0.81[CEU][hapmap]
rs28480636	0.83[EUR][1000 genomes]
rs4777789	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs734386	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7494944	0.87[EUR][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	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv524871	chr15:92690548-92704180	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6496897	SLCO3A1	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92645200-92705600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:92648200-92692600	Weak transcription	NHLF	lung
3	chr15:92649200-92710800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:92661000-92703600	Weak transcription	Small Intestine	intestine
5	chr15:92664000-92707000	Weak transcription	Liver	Liver
6	chr15:92664000-92712000	Weak transcription	Psoas Muscle	Psoas
7	chr15:92666000-92704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:92669600-92703000	Weak transcription	Brain Anterior Caudate	brain
9	chr15:92671600-92708000	Weak transcription	Gastric	stomach
10	chr15:92671800-92707800	Weak transcription	Colonic Mucosa	Colon
11	chr15:92671800-92709200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:92672000-92704200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:92672200-92695600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:92672200-92703200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:92673400-92692600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:92674800-92707800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:92678600-92692400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:92678600-92701000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:92679200-92698800	Weak transcription	Thymus	Thymus
20	chr15:92684000-92713200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:92684200-92701400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:92684400-92713200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:92684600-92701000	Weak transcription	NHEK	skin
24	chr15:92684800-92701400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:92685200-92701000	Weak transcription	HMEC	breast
26	chr15:92686000-92692400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:92686000-92703200	Weak transcription	Right Atrium	heart
28	chr15:92686400-92706800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:92686800-92707600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:92687400-92705000	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:92687600-92701000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:92687600-92719400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:92687800-92700400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:92688200-92692400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:92688400-92700400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:92689200-92693400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:92689200-92697600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr15:92689200-92697600	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:92689200-92700200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:92689400-92696200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:92689400-92697400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:92689400-92702400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:92689600-92697200	Strong transcription	Left Ventricle	heart
44	chr15:92689600-92706400	Weak transcription	HSMMtube	muscle
45	chr15:92689800-92698600	Strong transcription	Primary T cells from cord blood	blood
46	chr15:92689800-92702400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:92690000-92692400	Weak transcription	Fetal Heart	heart
48	chr15:92690200-92693600	Strong transcription	Ovary	ovary
49	chr15:92690200-92693800	Strong transcription	Spleen	Spleen
50	chr15:92690400-92707800	Weak transcription	Pancreas	Pancrea

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