Variant report

Variant	rs2253936
Chromosome Location	chr15:41805115-41805116
allele	A/G
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	SUZ12	chr15:41803702-41806103	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZBTB7A	chr15:41804970-41805280	K562	blood:	n/a	n/a
3	NR2F2	chr15:41804973-41805650	K562	blood:	n/a	n/a
4	EBF1	chr15:41805083-41805507	GM12878	blood:	n/a	chr15:41805281-41805292
5	HMGN3	chr15:41804926-41806286	K562	blood:	n/a	n/a
6	EBF1	chr15:41805097-41805504	GM12878	blood:	n/a	chr15:41805281-41805292
7	BHLHE40	chr15:41804763-41805522	GM12878	blood:	n/a	n/a
8	RUNX3	chr15:41805113-41805585	GM12878	blood:	n/a	n/a
9	MAX	chr15:41805059-41806606	NB4	blood:	n/a	n/a
10	MYC	chr15:41805100-41806613	NB4	blood:	n/a	n/a
11	GABPA	chr15:41805086-41805514	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr15:41805091-41805506	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41801767..41805579-chr15:41951979..41954300,3	K562	blood:
2	chr15:41803642..41805353-chr15:41818402..41820685,2	K562	blood:

Variant related genes	Relation type
LTK	TF binding region
ENSG00000174197	Chromatin interaction
ENSG00000103932	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1077809	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851405	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070331	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1200340	0.89[EUR][1000 genomes]
rs1200345	0.87[CHD][hapmap]
rs1200348	0.90[CHD][hapmap]
rs1200349	0.90[CHD][hapmap]
rs1867419	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274858	0.86[CHD][hapmap]
rs2289739	0.87[GIH][hapmap]
rs2289740	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297377	0.90[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2777490	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316622	0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs316623	0.92[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759793	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035331	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8035575	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv569233	chr15:41784809-41805237	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv33378	chr15:41786505-41805760	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2253936	NDUFAF1	cis	parietal	SCAN
rs2253936	RPAP1	cis	lymphoblastoid	seeQTL
rs2253936	TYRO3	cis	parietal	SCAN
rs2253936	SPTBN5	cis	parietal	SCAN
rs2253936	SPINT1	cis	parietal	SCAN
rs2253936	LTK	cis	lung	GTEx
rs2253936	NDUFAF1	cis	lymphoblastoid	seeQTL
rs2253936	BUB1B	cis	parietal	SCAN
rs2253936	RPAP1	cis	lymphoblastoid	GTEx
rs2253936	RPAP1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41801800-41819000	Weak transcription	Hela-S3	cervix
2	chr15:41803200-41806400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
3	chr15:41803200-41806400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:41803400-41806200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:41803400-41806400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr15:41803600-41805400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
7	chr15:41803600-41805400	Bivalent Enhancer	Fetal Heart	heart
8	chr15:41803600-41805600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr15:41803600-41806000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
10	chr15:41803600-41806200	Bivalent Enhancer	Fetal Brain Male	brain
11	chr15:41803600-41806200	Enhancers	Pancreas	Pancrea
12	chr15:41803600-41806200	Bivalent Enhancer	HMEC	breast
13	chr15:41803600-41806400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:41803800-41806200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:41803800-41806400	Bivalent Enhancer	Fetal Thymus	thymus
16	chr15:41804000-41805600	Bivalent/Poised TSS	Psoas Muscle	Psoas
17	chr15:41804000-41806200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
18	chr15:41804000-41806200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
19	chr15:41804000-41806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:41804000-41806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:41804000-41806400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
22	chr15:41804200-41805200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
23	chr15:41804200-41805200	Bivalent Enhancer	Left Ventricle	heart
24	chr15:41804200-41805400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:41804200-41805800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
26	chr15:41804200-41805800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
27	chr15:41804200-41806000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:41804200-41806200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
29	chr15:41804200-41806200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr15:41804200-41806200	Flanking Active TSS	Ovary	ovary
31	chr15:41804200-41806200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
33	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
34	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
37	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr15:41804400-41805200	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
39	chr15:41804400-41805200	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
40	chr15:41804400-41805200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
41	chr15:41804400-41805200	Bivalent Enhancer	Liver	Liver
42	chr15:41804400-41805200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
43	chr15:41804400-41805400	Bivalent Enhancer	Fetal Lung	lung
44	chr15:41804400-41805400	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
45	chr15:41804400-41805400	Flanking Bivalent TSS/Enh	NHEK	skin
46	chr15:41804400-41805600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
47	chr15:41804400-41805600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
48	chr15:41804400-41805800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
49	chr15:41804400-41806000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:41804400-41806000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain

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