Variant report

Variant	rs2240512
Chromosome Location	chr12:1753356-1753357
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	GATA2	chr12:1753012-1754336	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr12:1752997-1753364	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr12:1753310-1753484	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr12:1753051-1754439	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1751543..1753813-chr12:1771357..1773090,2	K562	blood:

Variant related genes	Relation type
WNT5B	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11061892	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240507	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2240508	0.90[ASN][1000 genomes]
rs2240509	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240511	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240513	0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs2240514	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2369972	0.90[ASN][1000 genomes]
rs3803164	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs6489314	0.87[JPT][hapmap]
rs735890	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs735891	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv898587	chr12:1732295-1756642	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv898588	chr12:1736314-1755960	Bivalent Enhancer Enhancers Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv898589	chr12:1738111-1755654	Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv898590	chr12:1740171-1757743	Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv898591	chr12:1745208-1755960	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv468964	chr12:1749905-1769930	Strong transcription Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv556995	chr12:1749905-1769930	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1739800-1753800	Weak transcription	Esophagus	oesophagus
2	chr12:1740600-1753400	Strong transcription	Osteobl	bone
3	chr12:1740600-1755000	Weak transcription	Spleen	Spleen
4	chr12:1740800-1753600	Weak transcription	Placenta	Placenta
5	chr12:1740800-1757400	Weak transcription	GM12878-XiMat	blood
6	chr12:1742000-1753400	Weak transcription	NHEK	skin
7	chr12:1743600-1759000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:1744200-1753400	Weak transcription	Adipose Nuclei	Adipose
9	chr12:1744400-1759000	Weak transcription	Right Ventricle	heart
10	chr12:1744600-1758000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:1745600-1753600	Weak transcription	Liver	Liver
12	chr12:1746600-1758000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:1747800-1754600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr12:1747800-1755800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:1747800-1756000	Weak transcription	K562	blood
16	chr12:1748000-1753400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:1748000-1753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:1748200-1753400	Weak transcription	HSMM	muscle
19	chr12:1749200-1760200	Weak transcription	Gastric	stomach
20	chr12:1749400-1753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:1749800-1753400	Weak transcription	Stomach Mucosa	stomach
22	chr12:1750000-1754800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:1750000-1766800	Weak transcription	Pancreas	Pancrea
24	chr12:1750200-1753400	Weak transcription	Ovary	ovary
25	chr12:1750200-1753600	Weak transcription	HSMMtube	muscle
26	chr12:1750600-1754800	Weak transcription	Thymus	Thymus
27	chr12:1751000-1755000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:1751400-1753800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:1751400-1753800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:1751800-1753600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:1751800-1754000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:1752000-1753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:1752000-1753600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:1752000-1753600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:1752000-1754000	Weak transcription	Fetal Intestine Small	intestine
36	chr12:1752000-1754800	Enhancers	Fetal Stomach	stomach
37	chr12:1752000-1769400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:1752200-1753600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:1752400-1755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:1752400-1755200	Enhancers	Fetal Heart	heart
41	chr12:1752400-1755600	Weak transcription	Fetal Intestine Large	intestine
42	chr12:1753000-1753400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:1753000-1753400	Enhancers	Brain Angular Gyrus	brain
44	chr12:1753000-1753600	Enhancers	Brain Substantia Nigra	brain
45	chr12:1753000-1753600	Enhancers	Colon Smooth Muscle	Colon
46	chr12:1753000-1753600	Flanking Active TSS	Fetal Brain Male	brain
47	chr12:1753000-1753800	Enhancers	Brain Anterior Caudate	brain
48	chr12:1753000-1754200	Enhancers	Rectal Smooth Muscle	rectum
49	chr12:1753000-1754400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:1753000-1754400	Flanking Active TSS	Fetal Brain Female	brain

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