Variant report

Variant	rs10880868
Chromosome Location	chr12:46322449-46322450
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	FOXA2	chr12:46322289-46322516	A549	lung:	n/a	n/a

Variant related genes	Relation type
SCAF11	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10880872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183212	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12580303	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12828693	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1978598	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7298844	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7310939	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7316454	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]

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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880868	SFRS2IP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46281400-46328800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:46290400-46325800	Weak transcription	Aorta	Aorta
3	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:46309400-46327400	Strong transcription	HSMM	muscle
5	chr12:46310200-46322600	Strong transcription	HSMMtube	muscle
6	chr12:46310400-46327200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:46310600-46327600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:46311000-46329000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:46311000-46329000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:46311200-46325200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:46311200-46328200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:46311200-46328600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:46311400-46327000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:46311400-46329000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:46311400-46329000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:46312000-46327800	Strong transcription	Osteobl	bone
17	chr12:46312000-46328800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:46312000-46329800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:46312000-46330000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:46312000-46330000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr12:46312200-46348600	Strong transcription	Dnd41	blood
22	chr12:46312400-46322800	Strong transcription	Primary B cells from cord blood	blood
23	chr12:46312400-46327400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr12:46312400-46327800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:46312400-46328200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:46312400-46329200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:46312600-46327000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:46312600-46327800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:46312800-46328800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:46313600-46326800	Strong transcription	Adipose Nuclei	Adipose
31	chr12:46313600-46326800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr12:46314000-46325000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:46314400-46322600	Strong transcription	Primary T cells from cord blood	blood
34	chr12:46314400-46328000	Strong transcription	Fetal Thymus	thymus
35	chr12:46314600-46326800	Strong transcription	Hela-S3	cervix
36	chr12:46314600-46327000	Strong transcription	Liver	Liver
37	chr12:46314600-46327600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:46314600-46345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:46314800-46325800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:46314800-46328400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:46315000-46327600	Weak transcription	Stomach Mucosa	stomach
42	chr12:46315000-46327800	Strong transcription	Fetal Intestine Large	intestine
43	chr12:46315000-46327800	Strong transcription	GM12878-XiMat	blood
44	chr12:46315000-46328800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:46315200-46323400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr12:46315200-46326600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:46315200-46327000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:46315200-46327600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:46315200-46327800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:46315400-46322800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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