Variant report

Variant	rs7923072
Chromosome Location	chr10:18938234-18938235
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165997	Chromatin interaction
ENSG00000152487	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10732437	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741086	1.00[CHB][hapmap]
rs10741120	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10741131	0.87[EUR][1000 genomes]
rs10764584	1.00[CHD][hapmap];0.81[YRI][hapmap]
rs10764587	1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs10764661	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828834	0.83[ASW][hapmap];0.82[CEU][hapmap];0.91[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs10828879	1.00[CHD][hapmap]
rs10828906	1.00[CHD][hapmap];0.80[MEX][hapmap];0.86[YRI][hapmap]
rs10829156	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829157	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829199	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917209	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1917823	0.82[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4316423	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4338439	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456162	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4475830	1.00[ASN][1000 genomes]
rs4484992	1.00[CHB][hapmap]
rs4606373	1.00[ASN][1000 genomes]
rs4634984	1.00[ASN][1000 genomes]
rs4636555	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4747353	0.85[YRI][hapmap]
rs4748476	1.00[CHB][hapmap]
rs4748479	1.00[ASN][1000 genomes]
rs4748493	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748494	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4748502	0.94[EUR][1000 genomes]
rs4748504	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748505	0.85[EUR][1000 genomes]
rs4748507	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62636215	0.89[ASN][1000 genomes]
rs6482516	1.00[CHD][hapmap]
rs6482534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6482545	0.89[ASN][1000 genomes]
rs6482546	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6482565	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6482567	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075678	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077786	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081271	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs7081435	1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082235	1.00[CHB][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs7084709	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7090926	0.89[ASN][1000 genomes]
rs7092437	1.00[CHB][hapmap]
rs7093907	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097534	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7098721	1.00[ASN][1000 genomes]
rs7099307	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7100884	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7895775	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7908550	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910506	1.00[CHD][hapmap]
rs7911922	1.00[ASN][1000 genomes]
rs7918933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8181345	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9731044	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7923072	NSUN6	cis	parietal	SCAN
rs7923072	RPP38	cis	cerebellum	SCAN
rs7923072	ARL5B	cis	cerebellum	SCAN
rs7923072	OLAH	cis	parietal	SCAN
rs7923072	NSUN6	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18916800-18938400	Weak transcription	HSMMtube	muscle
2	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
3	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
4	chr10:18917000-18938400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr10:18917000-18938400	Weak transcription	Ovary	ovary
6	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:18917000-18938400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:18917000-18938800	Weak transcription	HSMM	muscle
9	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
10	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:18917000-18940200	Weak transcription	Lung	lung
13	chr10:18921400-18939000	Weak transcription	Right Ventricle	heart
14	chr10:18922600-18939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:18925200-18939200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:18925600-18939400	Weak transcription	Brain Substantia Nigra	brain
17	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
18	chr10:18926200-18939200	Weak transcription	Fetal Kidney	kidney
19	chr10:18926400-18938600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:18927400-18939600	Weak transcription	Pancreas	Pancrea
21	chr10:18928000-18938400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr10:18928200-18939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr10:18928400-18938800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr10:18928800-18939600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:18928800-18939600	Weak transcription	Gastric	stomach
26	chr10:18929000-18939000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr10:18929600-18938800	Weak transcription	Fetal Intestine Large	intestine
28	chr10:18931000-18939600	Weak transcription	Fetal Muscle Leg	muscle
29	chr10:18932800-18938400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:18933200-18939400	Weak transcription	Thymus	Thymus
31	chr10:18934600-18939400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:18935400-18938600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:18935400-18938800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr10:18935800-18939200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:18936200-18938400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:18936400-18938400	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:18936400-18938800	Weak transcription	NH-A	brain
38	chr10:18936600-18938400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr10:18936800-18939400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr10:18937000-18938800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr10:18937000-18939000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr10:18937000-18939000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr10:18937000-18939000	Weak transcription	Fetal Intestine Small	intestine
44	chr10:18937000-18939600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr10:18937000-18939600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:18937000-18941400	Active TSS	GM12878-XiMat	blood
47	chr10:18937200-18938400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr10:18937200-18938400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:18937200-18938400	Weak transcription	Fetal Thymus	thymus
50	chr10:18937200-18938600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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