Variant report

Variant	rs2227311
Chromosome Location	chr13:48987032-48987033
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	KAP1	chr13:48987023-48987614	HEK293	kidney:	n/a	chr13:48987241-48987249
2	EP300	chr13:48987022-48987571	HepG2	liver:	n/a	chr13:48987250-48987264 chr13:48987069-48987083
3	POLR2A	chr13:48986920-48987561	HUVEC	blood vessel:	n/a	n/a
4	FOXA2	chr13:48987024-48987514	HepG2	liver:	n/a	n/a
5	NFIC	chr13:48986913-48987598	HepG2	liver:	n/a	n/a
6	POLR2A	chr13:48986754-48987547	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr13:48986993-48987537	HUVEC	blood vessel:	n/a	n/a
8	CREB1	chr13:48987019-48987617	HepG2	liver:	n/a	n/a
9	POLR2A	chr13:48986918-48987572	HepG2	liver:	n/a	n/a
10	FOXA1	chr13:48987010-48987598	HepG2	liver:	n/a	n/a
11	POLR2A	chr13:48986981-48987439	ProgFib	skin:	n/a	n/a
12	TCF7L2	chr13:48986962-48987472	HepG2	liver:	n/a	n/a
13	MYBL2	chr13:48986869-48987704	HepG2	liver:	n/a	n/a
14	MAX	chr13:48986994-48987622	HepG2	liver:	n/a	n/a
15	MBD4	chr13:48987011-48987598	HepG2	liver:	n/a	n/a
16	TCF12	chr13:48986982-48987620	A549	lung:	n/a	n/a
17	POLR2A	chr13:48986795-48987491	HepG2	liver:	n/a	n/a
18	POLR2A	chr13:48986196-48987715	MCF10A-Er-Src	breast:	n/a	n/a
19	REST	chr13:48987022-48987532	HepG2	liver:	n/a	n/a
20	POLR2A	chr13:48987014-48987504	HepG2	liver:	n/a	n/a
21	TBP	chr13:48987031-48987567	HepG2	liver:	n/a	n/a
22	EP300	chr13:48987013-48987571	HepG2	liver:	n/a	chr13:48987250-48987264 chr13:48987069-48987083
23	HEY1	chr13:48986928-48987581	HepG2	liver:	n/a	n/a
24	POLR2A	chr13:48987006-48987497	HUVEC	blood vessel:	n/a	n/a
25	STAT3	chr13:48986870-48987535	MCF10A-Er-Src	breast:	n/a	chr13:48987369-48987380
26	MYBL2	chr13:48987010-48987544	HepG2	liver:	n/a	n/a
27	CREB1	chr13:48987001-48987592	HepG2	liver:	n/a	n/a
28	FOXA1	chr13:48986938-48987631	HepG2	liver:	n/a	n/a
29	POLR2A	chr13:48986967-48987497	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr13:48987018-48987532	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
LPAR6	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12430215	1.00[YRI][hapmap]
rs3092877	0.82[YRI][hapmap]
rs4151450	0.82[YRI][hapmap]
rs4151510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316395	0.82[YRI][hapmap]
rs9316399	0.82[YRI][hapmap]
rs943278	0.82[YRI][hapmap]
rs9526479	0.82[YRI][hapmap]
rs9535020	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535021	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535032	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050786	chr13:48971510-48987032	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	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
rs2227311	NUDT15	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48976000-49005800	Weak transcription	Hela-S3	cervix
2	chr13:48978400-48989800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr13:48978800-48990400	Weak transcription	Spleen	Spleen
4	chr13:48981200-48987600	Active TSS	Right Atrium	heart
5	chr13:48982200-48987600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr13:48982400-48987200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:48983000-48987400	Active TSS	Brain Anterior Caudate	brain
8	chr13:48983000-48987600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:48983000-48987600	Active TSS	Brain Hippocampus Middle	brain
10	chr13:48983000-48987600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr13:48983000-48987800	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr13:48983400-48987400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:48983400-48987600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:48983400-48987600	Active TSS	Fetal Muscle Leg	muscle
15	chr13:48983400-48987600	Active TSS	Psoas Muscle	Psoas
16	chr13:48983400-48987800	Active TSS	GM12878-XiMat	blood
17	chr13:48983600-48987200	Active TSS	Thymus	Thymus
18	chr13:48983600-48987600	Active TSS	Rectal Smooth Muscle	rectum
19	chr13:48983800-48987400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr13:48983800-48987400	Active TSS	Monocytes-CD14+_RO01746	blood
21	chr13:48983800-48987600	Active TSS	HMEC	breast
22	chr13:48984000-48987200	Active TSS	Fetal Thymus	thymus
23	chr13:48984000-48987400	Active TSS	Primary T cells fromperipheralblood	blood
24	chr13:48984000-48987400	Active TSS	Liver	Liver
25	chr13:48984000-48987600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr13:48984200-48987200	Active TSS	Duodenum Mucosa	Duodenum
27	chr13:48984200-48987200	Active TSS	Placenta	Placenta
28	chr13:48984200-48987400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:48984200-48987400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:48984200-48987400	Active TSS	Brain Substantia Nigra	brain
31	chr13:48984200-48987400	Active TSS	Colon Smooth Muscle	Colon
32	chr13:48984200-48987400	Active TSS	Fetal Stomach	stomach
33	chr13:48984200-48987400	Active TSS	Stomach Smooth Muscle	stomach
34	chr13:48984200-48987600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:48984200-48987600	Active TSS	Brain Cingulate Gyrus	brain
36	chr13:48984200-48987600	Active TSS	NHDF-Ad	bronchial
37	chr13:48984200-48987600	Active TSS	NHLF	lung
38	chr13:48984400-48987200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:48984400-48987200	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr13:48984400-48987200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:48984400-48987400	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr13:48984400-48987400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:48984400-48987600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr13:48984400-48987600	Active TSS	Fetal Intestine Large	intestine
45	chr13:48984400-48987600	Active TSS	HSMMtube	muscle
46	chr13:48984400-48987800	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr13:48984600-48987200	Active TSS	Muscle Satellite Cultured Cells	--
48	chr13:48984600-48987200	Active TSS	Fetal Kidney	kidney
49	chr13:48984600-48987200	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr13:48984600-48987400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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