Variant report

Variant	rs7095070
Chromosome Location	chr10:18939070-18939071
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18938647..18942217-chr10:18945513..18950534,9	MCF-7	breast:
2	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: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10741099	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741100	0.82[EUR][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764584	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828835	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10829038	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829041	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10829042	0.80[EUR][1000 genomes]
rs10829133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015243	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11015263	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11015307	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11015411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015416	1.00[JPT][hapmap]
rs12359508	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12412484	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12569760	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12570585	0.95[ASN][1000 genomes]
rs12765362	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12772534	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1352655	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622920	1.00[JPT][hapmap]
rs1880682	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1968961	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1971272	1.00[JPT][hapmap]
rs2691159	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs4484992	0.94[YRI][hapmap]
rs4578284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4748474	0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4748489	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748491	0.81[AFR][1000 genomes]
rs4748495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4748503	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4748508	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482529	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6482534	0.93[YRI][hapmap]
rs7068575	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7070695	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	1.00[ASN][1000 genomes]
rs7071897	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7073651	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7075304	0.81[AFR][1000 genomes]
rs7077692	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	1.00[ASN][1000 genomes]
rs7081811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7082094	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7084525	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085332	0.90[ASN][1000 genomes]
rs7085587	0.90[ASN][1000 genomes]
rs7086034	0.90[ASN][1000 genomes]
rs7086911	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7088214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	1.00[ASN][1000 genomes]
rs7092437	0.93[YRI][hapmap]
rs7098313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7101352	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7895235	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895709	0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs7895775	0.87[YRI][hapmap]
rs7902450	1.00[JPT][hapmap]
rs7905730	1.00[JPT][hapmap]
rs7907153	0.92[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7917323	1.00[JPT][hapmap]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[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
rs7095070	RP11-499P20.2	cis	lung	GTEx
rs7095070	NSUN6	cis	Nerve Tibial	GTEx
rs7095070	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs7095070	NSUN6	cis	Skin Sun Exposed Lower leg	GTEx
rs7095070	NSUN6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18916800-18939800	Weak transcription	Aorta	Aorta
2	chr10:18916800-18940200	Weak transcription	Spleen	Spleen
3	chr10:18917000-18939600	Weak transcription	Placenta	Placenta
4	chr10:18917000-18939800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr10:18917000-18940200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:18917000-18940200	Weak transcription	Lung	lung
7	chr10:18922600-18939600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:18925200-18939200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr10:18925600-18939400	Weak transcription	Brain Substantia Nigra	brain
10	chr10:18926000-18940200	Weak transcription	Small Intestine	intestine
11	chr10:18926200-18939200	Weak transcription	Fetal Kidney	kidney
12	chr10:18927400-18939600	Weak transcription	Pancreas	Pancrea
13	chr10:18928200-18939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr10:18928800-18939600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr10:18928800-18939600	Weak transcription	Gastric	stomach
16	chr10:18931000-18939600	Weak transcription	Fetal Muscle Leg	muscle
17	chr10:18933200-18939400	Weak transcription	Thymus	Thymus
18	chr10:18934600-18939400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:18935800-18939200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr10:18936800-18939400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr10:18937000-18939600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr10:18937000-18939600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr10:18937000-18941400	Active TSS	GM12878-XiMat	blood
24	chr10:18937200-18939400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr10:18937200-18939400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:18937200-18939600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:18937200-18939600	Weak transcription	Left Ventricle	heart
28	chr10:18937400-18939600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr10:18937400-18939600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:18937600-18939600	Flanking Active TSS	Dnd41	blood
31	chr10:18937600-18941400	Active TSS	K562	blood
32	chr10:18937800-18939200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:18937800-18939200	Enhancers	Fetal Lung	lung
34	chr10:18937800-18940800	Active TSS	Liver	Liver
35	chr10:18937800-18941000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:18938000-18939200	Enhancers	Primary hematopoietic stem cells	blood
37	chr10:18938000-18939400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:18938200-18939200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:18938200-18939200	Enhancers	Primary B cells from cord blood	blood
40	chr10:18938200-18939200	Enhancers	Colon Smooth Muscle	Colon
41	chr10:18938200-18939200	Active TSS	Duodenum Mucosa	Duodenum
42	chr10:18938200-18939400	Enhancers	Fetal Stomach	stomach
43	chr10:18938200-18939600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:18938200-18939600	Enhancers	Primary B cells from peripheral blood	blood
45	chr10:18938200-18939800	Active TSS	Brain Angular Gyrus	brain
46	chr10:18938200-18940000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr10:18938200-18941200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr10:18938200-18941400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:18938400-18939200	Active TSS	Brain Hippocampus Middle	brain
50	chr10:18938400-18939200	Enhancers	Fetal Thymus	thymus

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