Variant report

Variant	rs2277537
Chromosome Location	chr15:41857080-41857081
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	chr15:41856390-41857223	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr15:41856229-41857524	K562	blood:	n/a	n/a
3	REST	chr15:41856176-41857362	H1-neurons	neurons:	n/a	chr15:41856892-41856905 chr15:41857166-41857184 chr15:41856895-41856908
4	CCNT2	chr15:41857032-41857519	K562	blood:	n/a	n/a
5	MAFK	chr15:41857013-41857137	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:41856706-41857290	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:41856429-41857237	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:41856414-41857086	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr15:41855023-41857639	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:41856338-41857405	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:41856102-41857580	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAZ	chr15:41856380-41857080	IMR90	lung:	n/a	n/a
13	POLR2A	chr15:41856390-41857107	K562	blood:	n/a	n/a
14	SP1	chr15:41856299-41857097	H1-hESC	embryonic stem cell:	n/a	chr15:41856720-41856731 chr15:41856481-41856495 chr15:41856793-41856802 chr15:41856851-41856865 chr15:41856708-41856719 chr15:41856789-41856803

No.	Distal block	Cell Line	Cell type
1	chr15:41856836..41858542-chr15:41952173..41953837,2	K562	blood:
2	chr15:41853373..41858542-chr15:41950830..41955637,10	K562	blood:
3	chr15:41849459..41853162-chr15:41854225..41857161,4	MCF-7	breast:

Variant related genes	Relation type
TYRO3	TF binding region
ENSG00000174197	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10438299	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1077714	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12906912	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12915829	0.82[AMR][1000 genomes]
rs2246444	0.92[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277536	0.91[ASN][1000 genomes]
rs2289743	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2482307	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28655000	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28657602	0.85[ASN][1000 genomes]
rs28792443	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28844285	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784283	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924552	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924554	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924556	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493004	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs6493005	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs66906913	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68058196	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7166371	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7183231	0.91[AMR][1000 genomes]
rs8025165	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3359172	chr15:41856320-41857334	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2277537	BMF	cis	cerebellum	SCAN
rs2277537	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs2277537	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs2277537	C15orf41	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41859600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:41852400-41860600	Weak transcription	HUVEC	blood vessel
4	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:41852600-41858600	Weak transcription	NHDF-Ad	bronchial
6	chr15:41852600-41859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:41852600-41877400	Weak transcription	HMEC	breast
8	chr15:41852800-41857600	Genic enhancers	Fetal Stomach	stomach
9	chr15:41852800-41877400	Weak transcription	NHEK	skin
10	chr15:41853000-41861800	Genic enhancers	Fetal Intestine Large	intestine
11	chr15:41853000-41862000	Genic enhancers	Fetal Intestine Small	intestine
12	chr15:41853200-41858200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:41853200-41860200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:41853200-41861800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr15:41853200-41863200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
17	chr15:41853400-41857400	Enhancers	Ovary	ovary
18	chr15:41853400-41859400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
19	chr15:41853400-41859800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
21	chr15:41853600-41857200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:41853600-41857600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
23	chr15:41853600-41859800	Genic enhancers	H1 Cell Line	embryonic stem cell
24	chr15:41853600-41860000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
28	chr15:41854000-41860200	Strong transcription	Dnd41	blood
29	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:41854200-41857800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr15:41854200-41859600	Weak transcription	Pancreas	Pancrea
33	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
34	chr15:41854400-41857600	Strong transcription	Fetal Brain Female	brain
35	chr15:41854600-41857200	Enhancers	Fetal Thymus	thymus
36	chr15:41854800-41857400	Genic enhancers	Fetal Muscle Leg	muscle
37	chr15:41855000-41857400	Genic enhancers	Fetal Lung	lung
38	chr15:41855000-41858200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:41855000-41861400	Genic enhancers	Brain Anterior Caudate	brain
40	chr15:41855200-41857400	Enhancers	Spleen	Spleen
41	chr15:41855200-41858000	Enhancers	Fetal Kidney	kidney
42	chr15:41855200-41858000	Weak transcription	A549	lung
43	chr15:41855200-41860000	Weak transcription	Gastric	stomach
44	chr15:41855400-41857400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41855400-41857400	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr15:41855400-41857600	Enhancers	Placenta	Placenta
47	chr15:41855400-41860200	Weak transcription	Esophagus	oesophagus
48	chr15:41855400-41862000	Weak transcription	NHLF	lung
49	chr15:41855400-41863400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:41855400-41864400	Genic enhancers	Brain Hippocampus Middle	brain

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