Variant report

Variant	rs12252040
Chromosome Location	chr10:89574902-89574903
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	MXI1	chr10:89574822-89579168	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89565566..89567376-chr10:89574790..89577127,2	K562	blood:
2	chr10:89560023..89562647-chr10:89574852..89577669,2	MCF-7	breast:

Variant related genes	Relation type
CFL1P1	TF binding region
ATAD1	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11202542	1.00[YRI][hapmap]
rs11202572	1.00[YRI][hapmap]
rs11202573	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12241293	1.00[YRI][hapmap]
rs12241491	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12258586	1.00[YRI][hapmap]
rs12262711	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7078640	0.83[AFR][1000 genomes]
rs73352882	0.83[AFR][1000 genomes]
rs73352883	0.85[AFR][1000 genomes]
rs73352889	0.83[AFR][1000 genomes]
rs7902457	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041462	chr10:89518729-89584284	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89473000-89577200	Weak transcription	Gastric	stomach
2	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
4	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
5	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
7	chr10:89527400-89575000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:89530800-89575800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:89537000-89576400	Weak transcription	HSMMtube	muscle
10	chr10:89541800-89575000	Weak transcription	Right Ventricle	heart
11	chr10:89543400-89577200	Weak transcription	Aorta	Aorta
12	chr10:89549400-89575400	Weak transcription	Brain Angular Gyrus	brain
13	chr10:89554400-89577200	Weak transcription	Pancreas	Pancrea
14	chr10:89557000-89575000	Weak transcription	Adipose Nuclei	Adipose
15	chr10:89557000-89575800	Weak transcription	NH-A	brain
16	chr10:89560600-89575000	Weak transcription	Small Intestine	intestine
17	chr10:89560800-89575600	Weak transcription	Fetal Brain Male	brain
18	chr10:89561600-89576600	Weak transcription	Fetal Kidney	kidney
19	chr10:89561800-89576200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:89562400-89575000	Weak transcription	Psoas Muscle	Psoas
21	chr10:89562400-89577400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:89562600-89575600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr10:89563000-89576600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:89563600-89575400	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:89563800-89576600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:89563800-89577400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:89564000-89575000	Weak transcription	Fetal Heart	heart
28	chr10:89564000-89577200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:89564400-89577200	Weak transcription	Lung	lung
30	chr10:89564800-89575600	Weak transcription	Brain Substantia Nigra	brain
31	chr10:89565200-89577000	Weak transcription	Ovary	ovary
32	chr10:89565600-89575000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:89565800-89576000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr10:89566000-89575000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr10:89567000-89575000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr10:89567400-89576200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr10:89568400-89576400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr10:89568800-89577000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr10:89569400-89575000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr10:89569800-89576800	Weak transcription	Fetal Stomach	stomach
41	chr10:89571000-89577200	Weak transcription	Esophagus	oesophagus
42	chr10:89572000-89575400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:89572000-89575600	Weak transcription	Brain Hippocampus Middle	brain
44	chr10:89572000-89575800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:89572600-89575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:89572600-89575000	Weak transcription	Fetal Intestine Large	intestine
47	chr10:89572600-89575600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr10:89572600-89576200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr10:89572600-89576200	Weak transcription	NHLF	lung
50	chr10:89572600-89576800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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