Variant report

Variant	rs4886874
Chromosome Location	chr15:77838086-77838087
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77837272..77839702-chr15:77860514..77863715,3	MCF-7	breast:
2	chr15:77837146..77840341-chr15:77840841..77844639,4	K562	blood:
3	chr15:77818777..77820332-chr15:77836618..77838168,2	MCF-7	breast:
4	chr15:77838034..77840169-chr15:77924048..77926294,2	K562	blood:

Variant related genes	Relation type
ENSG00000259420	Chromatin interaction
ENSG00000169783	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11855272	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856084	0.82[JPT][hapmap]
rs12324211	0.82[JPT][hapmap]
rs1317320	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs16953967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968895	0.89[JPT][hapmap]
rs16968897	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16968900	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16968930	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17394448	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs17471697	0.80[JPT][hapmap]
rs2137111	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs2307141	0.82[JPT][hapmap]
rs28375490	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28534698	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28712147	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784788	0.82[JPT][hapmap]
rs4243046	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61097729	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61483316	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7495653	0.84[ASN][1000 genomes]
rs869302	0.82[ASN][1000 genomes]
rs869310	0.83[ASN][1000 genomes]
rs907370	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907371	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907398	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886874	CYP1A2	cis	cerebellum	SCAN
rs4886874	PSTPIP1	cis	brain	seeQTL
rs4886874	PSTPIP1	cis	multi-tissue	Pritchard
rs4886874	STRA6	cis	cerebellum	SCAN
rs4886874	HMG20A	cis	parietal	SCAN
rs4886874	TSPAN3	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
2	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77833800-77843200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:77834000-77841200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:77834200-77840800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:77835800-77838200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:77836200-77838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:77836200-77838200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:77836200-77838200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:77836200-77838200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:77836200-77838200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:77836200-77838200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:77836200-77838200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:77836200-77838200	Weak transcription	Adipose Nuclei	Adipose
15	chr15:77836200-77838400	Weak transcription	HUVEC	blood vessel
16	chr15:77836200-77839000	Enhancers	Stomach Mucosa	stomach
17	chr15:77836200-77839600	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:77836200-77840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:77836200-77841000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:77836200-77841000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:77836200-77841000	Weak transcription	Fetal Thymus	thymus
22	chr15:77836200-77841200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:77836200-77841200	Weak transcription	K562	blood
24	chr15:77836200-77841400	Weak transcription	Brain Anterior Caudate	brain
25	chr15:77836200-77846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:77836400-77838200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:77836400-77838400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:77836400-77838400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:77836400-77838400	Weak transcription	GM12878-XiMat	blood
30	chr15:77836600-77838400	Weak transcription	Fetal Stomach	stomach
31	chr15:77836800-77838600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:77837000-77840400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:77837600-77838800	Enhancers	Gastric	stomach
34	chr15:77837600-77839000	Enhancers	NHLF	lung
35	chr15:77837800-77839000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:77837800-77839000	Enhancers	HSMM	muscle
37	chr15:77837800-77839000	Enhancers	HSMMtube	muscle
38	chr15:77837800-77839000	Enhancers	Osteobl	bone
39	chr15:77837800-77839200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:77837800-77839200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:77837800-77839800	Enhancers	Fetal Heart	heart
42	chr15:77838000-77838400	Enhancers	A549	lung
43	chr15:77838000-77838800	Enhancers	NHEK	skin
44	chr15:77838000-77839000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:77838000-77839000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:77838000-77839000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:77838000-77839000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:77838000-77839000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr15:77838000-77839000	Enhancers	Fetal Muscle Leg	muscle
50	chr15:77838000-77839000	Enhancers	Placenta	Placenta

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