Variant report

Variant	rs12791489
Chromosome Location	chr11:93234963-93234964
allele	A/G
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	GATA2	chr11:93234877-93235408	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
SMCO4	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11020387	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11020388	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11020390	0.97[EUR][1000 genomes]
rs11603107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603540	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603560	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11604399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11606505	0.97[EUR][1000 genomes]
rs11607585	0.97[EUR][1000 genomes]
rs12789912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12790221	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12795164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12796609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797006	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12806700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808363	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12808921	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305661	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2605596	0.83[ASN][1000 genomes]
rs2658797	0.83[ASN][1000 genomes]
rs28638787	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3207348	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34028949	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34580908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34716358	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34819559	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34825570	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35061570	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35364744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35368196	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35423935	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35548120	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35901746	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35930354	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3793999	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58462328	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6483248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483249	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66464546	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67927069	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7111773	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs7130465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71480681	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71480682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480685	0.85[EUR][1000 genomes]
rs7365	1.00[CHB][hapmap]
rs7928401	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7933953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7945684	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs897555	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs897558	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv522568	chr11:93231137-93239907	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv516461	chr11:93231476-93240847	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12791489	SMCO4	cis	Whole Blood	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93207000-93239000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:93209000-93235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
4	chr11:93211600-93243800	Weak transcription	Fetal Thymus	thymus
5	chr11:93218600-93254400	Weak transcription	Hela-S3	cervix
6	chr11:93218800-93238200	Weak transcription	Esophagus	oesophagus
7	chr11:93218800-93245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:93220800-93235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:93222400-93238000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:93222800-93236000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:93223000-93242800	Weak transcription	Adipose Nuclei	Adipose
12	chr11:93225400-93242800	Weak transcription	GM12878-XiMat	blood
13	chr11:93225600-93248800	Weak transcription	Fetal Muscle Leg	muscle
14	chr11:93226000-93235000	Weak transcription	Small Intestine	intestine
15	chr11:93226400-93257400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:93226600-93238000	Weak transcription	Fetal Lung	lung
17	chr11:93227000-93243800	Weak transcription	Lung	lung
18	chr11:93227200-93257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:93227400-93239800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:93227800-93235000	Weak transcription	Pancreas	Pancrea
21	chr11:93228200-93243400	Weak transcription	Right Ventricle	heart
22	chr11:93228200-93248200	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:93228400-93235000	Weak transcription	HepG2	liver
24	chr11:93228400-93237800	Weak transcription	Osteobl	bone
25	chr11:93229800-93235000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:93231000-93236600	Weak transcription	Dnd41	blood
27	chr11:93231600-93235200	Strong transcription	Aorta	Aorta
28	chr11:93232200-93243200	Weak transcription	Spleen	Spleen
29	chr11:93232400-93237400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:93232400-93237800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:93232400-93238800	Weak transcription	Ovary	ovary
32	chr11:93232400-93245200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:93232600-93235800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:93232600-93236200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr11:93232800-93235000	Weak transcription	Fetal Intestine Small	intestine
36	chr11:93232800-93236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:93232800-93236600	Weak transcription	Fetal Stomach	stomach
38	chr11:93232800-93237800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:93232800-93243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:93232800-93245800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:93232800-93248800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:93233000-93248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:93233000-93248800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:93233000-93257400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:93233200-93241200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:93233400-93236000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:93233400-93248600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:93234000-93242600	Enhancers	Liver	Liver
49	chr11:93234200-93240800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr11:93234400-93237400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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