Variant report

Variant	rs869884
Chromosome Location	chr15:77291598-77291599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77282963..77284982-chr15:77290568..77292460,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12900395	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs17380886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17465692	0.90[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap]
rs2458245	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs2458247	0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2469229	0.85[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs34220530	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34370173	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34500166	0.81[EUR][1000 genomes]
rs35018118	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4886508	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1808532	chr15:77257714-77332539	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1043017	chr15:77266776-77309938	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1035874	chr15:77266776-77328742	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv1822592	chr15:77283956-77332539	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv570111	chr15:77286693-77332606	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription 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	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs869884	NEO1	cis	cerebellum	SCAN
rs869884	CRABP1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77288200-77293600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:77289200-77311200	Weak transcription	Aorta	Aorta
3	chr15:77289400-77292800	Enhancers	Fetal Thymus	thymus
4	chr15:77289400-77299000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:77289400-77302200	Weak transcription	Pancreas	Pancrea
6	chr15:77289400-77305200	Weak transcription	Esophagus	oesophagus
7	chr15:77289400-77310000	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:77289600-77293400	Weak transcription	Spleen	Spleen
9	chr15:77289600-77294400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:77289600-77294400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:77289600-77294800	Weak transcription	HSMM	muscle
12	chr15:77289600-77295000	Weak transcription	Colonic Mucosa	Colon
13	chr15:77289600-77301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:77289800-77294400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:77289800-77294400	Weak transcription	Thymus	Thymus
16	chr15:77289800-77294600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:77289800-77296200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:77289800-77297400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:77290000-77292000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:77290000-77294400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:77290200-77293800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:77290200-77294000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:77290200-77306000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:77290400-77292000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr15:77290600-77291600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr15:77290800-77291800	Enhancers	Primary T cells from cord blood	blood
27	chr15:77290800-77292000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:77290800-77293800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:77291000-77291600	Enhancers	Fetal Muscle Leg	muscle
30	chr15:77291000-77291600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
31	chr15:77291000-77291800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:77291000-77295000	Genic enhancers	Primary monocytes fromperipheralblood	blood
33	chr15:77291000-77295200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:77291200-77291600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:77291200-77291600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr15:77291200-77291600	Enhancers	GM12878-XiMat	blood
37	chr15:77291200-77293200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr15:77291200-77293400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:77291200-77293600	Weak transcription	Placenta	Placenta
40	chr15:77291200-77299600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr15:77291400-77291600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr15:77291400-77291600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:77291400-77292200	Weak transcription	Primary B cells from cord blood	blood
44	chr15:77291400-77292400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:77291400-77293000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
46	chr15:77291400-77293200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr15:77291400-77293600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:77291400-77295000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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