Variant report

Variant	rs12631075
Chromosome Location	chr3:100210775-100210776
allele	A/C
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	chr3:100210600-100211815	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:100210641-100211845	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:100210775-100211951	HepG2	liver:	n/a	n/a
4	PBX3	chr3:100210759-100211738	SK-N-SH	brain:	n/a	chr3:100211366-100211375 chr3:100211351-100211371 chr3:100210771-100210782
5	SP1	chr3:100210774-100211580	H1-hESC	embryonic stem cell:	n/a	chr3:100211328-100211337 chr3:100211326-100211338 chr3:100211326-100211338 chr3:100211364-100211385 chr3:100211016-100211026
6	E2F6	chr3:100210687-100211716	H1-hESC	embryonic stem cell:	n/a	chr3:100211365-100211374 chr3:100210711-100210718
7	NFYB	chr3:100210702-100211955	GM12878	blood:	n/a	chr3:100211396-100211406 chr3:100211363-100211378 chr3:100211360-100211375 chr3:100211363-100211377 chr3:100211391-100211406 chr3:100211362-100211374 chr3:100211363-100211378
8	TAF1	chr3:100210701-100211695	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr3:100210746-100211820	A549	lung:	n/a	chr3:100211520-100211529
10	POLR2A	chr3:100210615-100211748	HUVEC	blood vessel:	n/a	n/a
11	CHD2	chr3:100210730-100211741	GM12878	blood:	n/a	n/a
12	MXI1	chr3:100210419-100212102	IMR90	lung:	n/a	n/a
13	KAP1	chr3:100210739-100211465	HEK293	kidney:	n/a	n/a
14	WRNIP1	chr3:100210745-100211420	GM12878	blood:	n/a	n/a
15	REST	chr3:100210660-100211671	H1-neurons	neurons:	n/a	chr3:100211017-100211030 chr3:100211237-100211250
16	HA-E2F1	chr3:100210693-100211735	MCF-7	breast:	n/a	chr3:100211365-100211374 chr3:100210711-100210718
17	POLR2A	chr3:100210705-100212217	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:100210701-100211899	SK-N-SH	brain:	n/a	n/a
19	ZNF143	chr3:100210734-100211556	H1-hESC	embryonic stem cell:	n/a	chr3:100211186-100211196
20	POLR2A	chr3:100210721-100211826	U87	brain:	n/a	n/a
21	MAZ	chr3:100210653-100211975	IMR90	lung:	n/a	chr3:100211520-100211529
22	HCFC1	chr3:100210634-100212018	Hela-S3	cervix:	n/a	n/a
23	EBF1	chr3:100210725-100211862	GM12878	blood:	n/a	chr3:100210924-100210935 chr3:100210924-100210937 chr3:100210962-100210971 chr3:100210926-100210935 chr3:100210926-100210935 chr3:100211295-100211305 chr3:100210925-100210935
24	EBF1	chr3:100210768-100211067	GM12878	blood:	n/a	chr3:100210924-100210935 chr3:100210924-100210937 chr3:100210962-100210971 chr3:100210926-100210935 chr3:100210926-100210935 chr3:100210925-100210935
25	JUND	chr3:100210771-100211638	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:100210418-100212116	IMR90	lung:	n/a	n/a
27	POLR2A	chr3:100210737-100212005	U87	brain:	n/a	n/a
28	POLR2A	chr3:100210758-100211674	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:100210560-100212011	U87	brain:	n/a	n/a
30	SPI1	chr3:100210618-100210884	GM12891	blood:	n/a	n/a
31	NRF1	chr3:100210695-100211674	SK-N-SH	brain:	n/a	n/a
32	SIN3A	chr3:100210673-100211793	H1-hESC	embryonic stem cell:	n/a	chr3:100211247-100211258
33	POLR2A	chr3:100210769-100211699	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
TMEM45A	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11923942	0.89[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11927516	0.89[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12634371	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636452	0.91[MEX][hapmap]
rs12636805	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12639465	0.89[CEU][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs4928097	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4928110	0.91[MEX][hapmap]
rs4928111	0.81[AMR][1000 genomes]
rs57018910	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58789183	0.81[AMR][1000 genomes]
rs59299896	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60071944	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60272820	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61636409	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276517	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276520	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62276521	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62276522	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62276523	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276526	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62276556	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62276559	0.88[EUR][1000 genomes]
rs66791174	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67600559	0.94[EUR][1000 genomes]
rs6763079	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6763178	0.82[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67774605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6798264	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73152126	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7429072	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7429277	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7429604	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430698	1.00[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7430715	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7431846	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7616839	0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7640470	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7653196	0.83[MEX][hapmap]
rs9851429	0.89[CEU][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.92[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	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12631075	TMEM45A	cis	parietal	SCAN
rs12631075	TMEM45A	cis	Whole Blood	GTEx
rs12631075	OR5K4	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100205000-100210800	Weak transcription	K562	blood
2	chr3:100209600-100210800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:100210000-100210800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr3:100210200-100210800	Weak transcription	Psoas Muscle	Psoas
5	chr3:100210400-100210800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:100210400-100210800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:100210400-100210800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:100210400-100210800	Flanking Active TSS	NHLF	lung
9	chr3:100210400-100211000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:100210400-100211000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:100210400-100211000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:100210400-100211000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:100210400-100211000	Flanking Active TSS	Liver	Liver
14	chr3:100210400-100211000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
15	chr3:100210400-100211000	Flanking Active TSS	Fetal Lung	lung
16	chr3:100210400-100211000	Flanking Active TSS	Fetal Stomach	stomach
17	chr3:100210400-100212200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:100210400-100212200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:100210400-100212600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:100210400-100212600	Active TSS	Brain Anterior Caudate	brain
21	chr3:100210600-100210800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:100210600-100210800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
23	chr3:100210600-100210800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:100210600-100210800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:100210600-100210800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:100210600-100210800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:100210600-100210800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:100210600-100210800	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:100210600-100210800	Active TSS	Colonic Mucosa	Colon
30	chr3:100210600-100210800	Active TSS	Fetal Brain Male	brain
31	chr3:100210600-100210800	Flanking Active TSS	Fetal Brain Female	brain
32	chr3:100210600-100210800	Flanking Active TSS	Fetal Kidney	kidney
33	chr3:100210600-100210800	Enhancers	Placenta	Placenta
34	chr3:100210600-100210800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:100210600-100210800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
36	chr3:100210600-100210800	Flanking Active TSS	NHDF-Ad	bronchial
37	chr3:100210600-100211000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:100210600-100211000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:100210600-100211000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr3:100210600-100211000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:100210600-100211000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:100210600-100211000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:100210600-100211000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:100210600-100211000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr3:100210600-100211000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:100210600-100211000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr3:100210600-100211000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:100210600-100211000	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr3:100210600-100211000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr3:100210600-100211000	Flanking Active TSS	Fetal Intestine Large	intestine

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