Variant report

Variant	rs1838572
Chromosome Location	chr10:49759366-49759367
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	CTCF	chr10:49759280-49759430	HCFaa	heart:	n/a	chr10:49759297-49759305
2	EP300	chr10:49758900-49760644	SK-N-SH	brain:	n/a	chr10:49760537-49760546 chr10:49760441-49760457 chr10:49760610-49760619
3	RAD21	chr10:49759317-49760650	SK-N-SH	brain:	n/a	chr10:49759730-49759749 chr10:49760623-49760632 chr10:49760454-49760464 chr10:49760621-49760631
4	CTCF	chr10:49758881-49760623	SK-N-SH	brain:	n/a	chr10:49759297-49759305 chr10:49760416-49760429 chr10:49759729-49759747 chr10:49759731-49759752
5	CTCF	chr10:49759280-49759430	HFF	foreskin:	n/a	chr10:49759297-49759305
6	CTCF	chr10:49759220-49759370	MCF-7	breast:	n/a	chr10:49759297-49759305
7	CTCF	chr10:49759240-49759390	GM12868	blood:	n/a	chr10:49759297-49759305

No.	Distal block	Cell Line	Cell type
1	chr10:49755429..49757315-chr10:49758822..49761538,2	K562	blood:
2	chr10:49758981..49760739-chr10:49863487..49865066,35	MCF-7	breast:
3	chr10:49759298..49760794-chr10:49863704..49864896,18	K562	blood:

Variant related genes	Relation type
ENSG00000231906	TF binding region
ENSG00000128805	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1078261	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11101383	1.00[ASN][1000 genomes]
rs11598598	1.00[CHB][hapmap]
rs12766573	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1373795	1.00[CHB][hapmap]
rs1445150	0.86[CEU][hapmap]
rs1838571	0.85[CEU][hapmap]
rs2004665	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838619	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4838620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537567	0.85[CEU][hapmap]
rs7077561	0.87[EUR][1000 genomes]
rs7092639	0.92[CEU][hapmap]
rs7093632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs747532	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7895981	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7911418	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7919520	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs935265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs935268	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs935269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935270	1.00[JPT][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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49734400-49762400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:49739400-49762400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:49742600-49774800	Weak transcription	Aorta	Aorta
4	chr10:49751200-49771600	Weak transcription	Pancreas	Pancrea
5	chr10:49751400-49759600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:49752200-49760200	Strong transcription	HSMM	muscle
7	chr10:49753000-49760200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr10:49753200-49760200	Strong transcription	Osteobl	bone
9	chr10:49753400-49759600	Strong transcription	NHLF	lung
10	chr10:49753400-49764400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:49753800-49759600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:49755000-49761800	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:49756000-49760000	Weak transcription	Ovary	ovary
14	chr10:49756200-49759600	Weak transcription	Brain Angular Gyrus	brain
15	chr10:49756200-49759800	Weak transcription	Fetal Lung	lung
16	chr10:49756400-49759800	Weak transcription	Brain Anterior Caudate	brain
17	chr10:49756400-49759800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr10:49756600-49759800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:49756800-49759400	Weak transcription	Brain Substantia Nigra	brain
20	chr10:49757000-49759600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr10:49757000-49759800	Weak transcription	Brain Hippocampus Middle	brain
22	chr10:49757200-49760200	Strong transcription	NHDF-Ad	bronchial
23	chr10:49757400-49759800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:49757400-49760400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:49757400-49761600	Enhancers	HUVEC	blood vessel
26	chr10:49757400-49782200	Weak transcription	HSMMtube	muscle
27	chr10:49757800-49759800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:49758200-49762400	Weak transcription	Right Atrium	heart
29	chr10:49758400-49759800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:49758400-49762200	Weak transcription	HMEC	breast
31	chr10:49758600-49762000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:49758800-49759800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr10:49759000-49760800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr10:49759000-49761400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr10:49759200-49759600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:49759200-49760400	Enhancers	Fetal Thymus	thymus
37	chr10:49759200-49761000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:49759200-49761200	Enhancers	Primary B cells from peripheral blood	blood
39	chr10:49759200-49770400	Weak transcription	NH-A	brain

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