Variant report

Variant	rs4993294
Chromosome Location	chr12:49883204-49883205
allele	G/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	PBX3	chr12:49882880-49883363	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr12:49882781-49884326	SK-N-SH	brain:	n/a	chr12:49883538-49883554 chr12:49883794-49883804 chr12:49883536-49883557 chr12:49883797-49883804 chr12:49883541-49883550
3	EP300	chr12:49883004-49884009	SK-N-SH_RA	brain:	n/a	chr12:49883597-49883606
4	GATA3	chr12:49882804-49884441	SK-N-SH	brain:	n/a	chr12:49883538-49883554 chr12:49883794-49883804 chr12:49883536-49883557 chr12:49883797-49883804 chr12:49883541-49883550
5	TCF12	chr12:49882848-49884190	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr12:49882912-49884217	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr12:49882780-49884247	SK-N-SH	brain:	n/a	n/a
8	PBX3	chr12:49882940-49884181	SK-N-SH	brain:	n/a	n/a
9	FOS	chr12:49883185-49883993	HUVEC	blood vessel:	n/a	chr12:49883769-49883779 chr12:49883770-49883778
10	EP300	chr12:49882960-49884113	SK-N-SH	brain:	n/a	chr12:49883597-49883606
11	FOSL2	chr12:49882905-49884135	SK-N-SH	brain:	n/a	chr12:49883769-49883779 chr12:49883770-49883778

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49759096..49761213-chr12:49881834..49884299,3	K562	blood:

Variant related genes	Relation type
SPATS2	TF binding region
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10783314	1.00[CHB][hapmap]
rs11169043	0.81[ASN][1000 genomes]
rs11169045	0.81[ASN][1000 genomes]
rs11169063	0.86[CHD][hapmap]
rs11169065	1.00[CHB][hapmap]
rs11169069	1.00[CHB][hapmap]
rs11169073	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11169080	0.86[CHD][hapmap]
rs11169081	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11169082	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11169092	1.00[CHB][hapmap]
rs11169097	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11169104	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11169106	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11615710	0.81[ASN][1000 genomes]
rs11833411	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs11834380	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs12299505	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs12303310	1.00[CHB][hapmap]
rs12310510	1.00[CHB][hapmap]
rs12311839	1.00[CHB][hapmap]
rs12321819	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs13906	1.00[CHB][hapmap]
rs17123808	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs1902329	1.00[CHB][hapmap]
rs1902330	1.00[CHB][hapmap]
rs2278068	1.00[CHB][hapmap]
rs2278069	1.00[CHB][hapmap]
rs2303305	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs35275181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3815832	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs3887727	0.86[CHD][hapmap]
rs3887728	1.00[CHB][hapmap]
rs4133070	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs56322609	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57202083	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58125498	0.81[ASN][1000 genomes]
rs59689618	0.96[ASN][1000 genomes]
rs60418472	0.82[AFR][1000 genomes]
rs61375453	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131915	1.00[CHB][hapmap]
rs7133398	0.84[CHD][hapmap]
rs7295556	0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs7296281	1.00[CHB][hapmap]
rs7301209	1.00[CHB][hapmap]
rs74088737	0.84[AFR][1000 genomes]
rs74089508	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74089512	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74089515	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74089517	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089520	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952734	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7953911	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7954994	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7956181	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7962863	0.86[CHD][hapmap]
rs7965658	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7970241	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7973389	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7975599	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7975712	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs7977389	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs8626	0.86[CHD][hapmap]
rs876889	1.00[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
3	chr12:49850400-49911000	Weak transcription	K562	blood
4	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
5	chr12:49856400-49883400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:49856600-49890200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:49856600-49890200	Weak transcription	Ovary	ovary
8	chr12:49856800-49883600	Weak transcription	Dnd41	blood
9	chr12:49856800-49898400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:49859400-49883400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:49859400-49888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:49869600-49890000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:49870200-49884600	Weak transcription	Spleen	Spleen
15	chr12:49872200-49895000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:49873000-49890400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:49873000-49918800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:49873200-49918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:49873800-49904600	Weak transcription	Fetal Heart	heart
20	chr12:49874000-49889800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:49874000-49904400	Weak transcription	Fetal Brain Male	brain
22	chr12:49874200-49890600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:49874800-49914200	Weak transcription	Fetal Kidney	kidney
24	chr12:49876400-49894800	Weak transcription	Fetal Intestine Large	intestine
25	chr12:49876400-49897600	Weak transcription	Small Intestine	intestine
26	chr12:49876400-49911200	Weak transcription	Adipose Nuclei	Adipose
27	chr12:49876600-49890000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:49876600-49893200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:49876800-49888400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:49876800-49890000	Weak transcription	NHLF	lung
31	chr12:49876800-49890200	Weak transcription	Fetal Thymus	thymus
32	chr12:49876800-49890400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:49876800-49898000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:49876800-49905200	Weak transcription	Right Ventricle	heart
35	chr12:49876800-49916200	Weak transcription	Psoas Muscle	Psoas
36	chr12:49877000-49893000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:49877000-49908800	Weak transcription	NHDF-Ad	bronchial
38	chr12:49877000-49909000	Weak transcription	Brain Germinal Matrix	brain
39	chr12:49877200-49885200	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:49877600-49902000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:49877800-49883400	Weak transcription	HepG2	liver
42	chr12:49877800-49885200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:49877800-49889600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:49878000-49883600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:49878000-49893600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:49878200-49892400	Weak transcription	Liver	Liver
47	chr12:49878600-49890200	Weak transcription	Brain Angular Gyrus	brain
48	chr12:49878600-49918600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr12:49878800-49883400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:49879600-49890000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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