Variant report

Variant	rs1881740
Chromosome Location	chr10:49551560-49551561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49516332..49518147-chr10:49551001..49553402,2	MCF-7	breast:
2	chr10:49523430..49525253-chr10:49550597..49552808,2	K562	blood:
3	chr10:49513460..49515934-chr10:49549553..49551759,2	K562	blood:

Variant related genes	Relation type
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10745265	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10776592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10776593	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10776594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857563	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857564	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11101284	0.86[GIH][hapmap]
rs11101285	1.00[JPT][hapmap]
rs11101326	0.84[CEU][hapmap];0.83[CHD][hapmap]
rs1112268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11597435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11598320	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12358297	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17780725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1881735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1881737	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881738	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1919706	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1919707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1919709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1997365	0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2141516	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178339	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2377140	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377141	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2377143	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs2377349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590382	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2590383	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590384	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2590385	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2590386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2698758	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2698762	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2698768	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2889595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813864	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs4012930	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4838404	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs4838405	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4838588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56078229	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6537559	0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7068398	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7084326	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7097975	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs7898026	0.83[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9919504	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	nsv6587	chr10:49526329-49571804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1881740	MSMB	cis	parietal	SCAN
rs1881740	ANTXRL	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49516400-49559600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:49525800-49551800	Weak transcription	Adipose Nuclei	Adipose
3	chr10:49526200-49552000	Weak transcription	NH-A	brain
4	chr10:49530800-49554600	Weak transcription	Fetal Brain Male	brain
5	chr10:49539000-49551800	Weak transcription	NHLF	lung
6	chr10:49539200-49555000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:49539600-49553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:49540400-49554000	Weak transcription	Pancreas	Pancrea
9	chr10:49540600-49551800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:49540800-49551600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr10:49541000-49551800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr10:49541000-49551800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr10:49541000-49554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:49541200-49559400	Weak transcription	Fetal Lung	lung
15	chr10:49541400-49553800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:49542000-49554000	Weak transcription	Fetal Thymus	thymus
17	chr10:49542800-49551800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:49542800-49552000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:49542800-49568000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:49543000-49551800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr10:49543000-49553800	Weak transcription	Right Ventricle	heart
22	chr10:49543000-49576200	Weak transcription	Right Atrium	heart
23	chr10:49543200-49552000	Weak transcription	Primary B cells from cord blood	blood
24	chr10:49543200-49554800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:49543200-49554800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr10:49545400-49552000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:49545800-49555800	Weak transcription	Primary T cells from cord blood	blood
28	chr10:49547000-49553600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:49548400-49551800	Weak transcription	GM12878-XiMat	blood
30	chr10:49548800-49551600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:49549000-49557000	Weak transcription	HSMMtube	muscle
32	chr10:49549200-49555200	Weak transcription	Dnd41	blood
33	chr10:49550200-49552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:49550200-49553800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:49550400-49560800	Weak transcription	Psoas Muscle	Psoas
36	chr10:49551000-49551800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:49551000-49552200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr10:49551000-49552600	Enhancers	Fetal Heart	heart
39	chr10:49551000-49552600	Enhancers	Left Ventricle	heart
40	chr10:49551200-49551600	Enhancers	Ovary	ovary
41	chr10:49551200-49552000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr10:49551200-49552000	Enhancers	Brain Hippocampus Middle	brain
43	chr10:49551200-49552200	Enhancers	Brain Substantia Nigra	brain
44	chr10:49551200-49552600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:49551200-49552600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr10:49551200-49552600	Enhancers	NHDF-Ad	bronchial
47	chr10:49551400-49551800	Weak transcription	Aorta	Aorta
48	chr10:49551400-49552200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr10:49551400-49552600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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