Variant report

Variant	rs12631733
Chromosome Location	chr3:112991117-112991118
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	GATA1	chr3:112990664-112991660	PBDE	blood:	n/a	n/a
2	RCOR1	chr3:112990855-112991205	K562	blood:	n/a	n/a
3	CCNT2	chr3:112990964-112991195	K562	blood:	n/a	n/a
4	CEBPD	chr3:112990878-112991298	K562	blood:	n/a	n/a
5	TAL1	chr3:112990851-112991224	K562	blood:	n/a	n/a
6	TEAD4	chr3:112990858-112991160	K562	blood:	n/a	n/a
7	GATA1	chr3:112990802-112991183	K562	blood:	n/a	n/a
8	MYC	chr3:112990891-112991134	K562	blood:	n/a	n/a
9	JUND	chr3:112990994-112991153	K562	blood:	n/a	n/a

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10511323	0.84[EUR][1000 genomes]
rs11710894	0.85[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11717833	0.85[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919134	0.80[CHD][hapmap];0.86[MEX][hapmap]
rs12485329	0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs12492273	0.90[CHB][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs12494864	0.90[CHB][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12638030	0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16860758	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16860787	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2036282	0.90[CHB][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs34284771	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3814398	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3846046	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3856718	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3856719	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3856720	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682131	0.84[EUR][1000 genomes]
rs4682132	0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682478	0.84[EUR][1000 genomes]
rs4682479	0.90[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4682481	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682483	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73235143	0.84[EUR][1000 genomes]
rs73235147	0.83[EUR][1000 genomes]
rs7641410	0.84[EUR][1000 genomes]
rs775222	0.84[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS 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 miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12631733	CD96	cis	cerebellum	SCAN
rs12631733	BOC	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
6	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:112982800-112993600	Weak transcription	HMEC	breast
10	chr3:112983800-112995000	Weak transcription	Lung	lung
11	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
12	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:112984200-112994400	Weak transcription	HSMM	muscle
14	chr3:112984600-112991200	Weak transcription	Brain Germinal Matrix	brain
15	chr3:112984600-112993400	Weak transcription	Fetal Brain Male	brain
16	chr3:112984800-112992400	Weak transcription	Fetal Thymus	thymus
17	chr3:112984800-112993000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:112985400-112993600	Strong transcription	Fetal Lung	lung
21	chr3:112986200-112994200	Strong transcription	Ovary	ovary
22	chr3:112986400-112993000	Strong transcription	Fetal Intestine Small	intestine
23	chr3:112986400-112994600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:112986600-112993800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:112987200-112993400	Strong transcription	Fetal Stomach	stomach
26	chr3:112987200-112994400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:112987400-112991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:112987800-112991200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
30	chr3:112988000-112992200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:112988000-112993600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:112988000-112993800	Weak transcription	Brain Angular Gyrus	brain
33	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr3:112988200-112992600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:112988200-112993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:112988200-112993600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:112988200-112993800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:112988200-112994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:112988200-112994200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:112988200-112994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:112988400-112991600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:112988400-112994000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:112988400-112994600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
45	chr3:112989000-112993000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:112989000-112993600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:112989000-112994000	Weak transcription	Brain Anterior Caudate	brain
48	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:112989200-112993600	Strong transcription	Rectal Smooth Muscle	rectum
50	chr3:112989400-112992000	Strong transcription	Adipose Nuclei	Adipose

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