Variant report

Variant	rs3813905
Chromosome Location	chr16:70680850-70680851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:70556330..70559172-chr16:70679219..70681139,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SF3B3-2	chr16:70680776-70680878	NONHSAT143438

Variant related genes	Relation type
ENSG00000189091	Chromatin interaction
ENSG00000103051	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11865804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11866403	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12596070	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12596475	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12598251	0.80[ASN][1000 genomes]
rs12598456	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12598945	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12598955	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12919296	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12919451	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12920334	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12920529	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12923477	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12923630	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12923637	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12924304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12925493	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12926402	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12929463	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12929508	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12935541	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13329733	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1551530	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16970408	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1973089	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1973090	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs33998678	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34426756	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34644948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34692833	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34811595	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34881169	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35283920	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35285555	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35290416	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35381200	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35437297	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35794088	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36097154	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985413	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985414	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4985415	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985546	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985549	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985550	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985551	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985552	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4985553	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55872380	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56220651	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57738457	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57752020	0.84[AMR][1000 genomes]
rs59865481	0.84[AMR][1000 genomes]
rs61170208	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68049363	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71401818	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7191249	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7192723	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7198170	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8060584	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8061329	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9933834	0.84[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906874	chr16:70677785-70740707	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906875	chr16:70677785-70742536	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
8	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70669600-70687800	Weak transcription	Right Atrium	heart
2	chr16:70673600-70683200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:70673600-70684000	Weak transcription	Esophagus	oesophagus
4	chr16:70673800-70682800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr16:70678000-70681200	Weak transcription	Fetal Intestine Large	intestine
6	chr16:70679600-70681000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:70679600-70681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr16:70679800-70681200	Enhancers	Placenta	Placenta
9	chr16:70679800-70682400	Enhancers	Fetal Brain Male	brain
10	chr16:70680000-70681000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr16:70680000-70681000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr16:70680000-70682000	Enhancers	Fetal Muscle Leg	muscle
13	chr16:70680000-70687200	Strong transcription	Fetal Intestine Small	intestine
14	chr16:70680200-70681000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr16:70680200-70681000	Flanking Active TSS	Fetal Brain Female	brain
16	chr16:70680200-70681200	Genic enhancers	Fetal Stomach	stomach
17	chr16:70680200-70681400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr16:70680200-70681400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr16:70680200-70681800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:70680200-70681800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:70680200-70681800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr16:70680200-70681800	Enhancers	Ovary	ovary
23	chr16:70680200-70683400	Active TSS	Brain Angular Gyrus	brain
24	chr16:70680400-70681400	Active TSS	Stomach Smooth Muscle	stomach
25	chr16:70680400-70681600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr16:70680400-70683600	Active TSS	Brain Hippocampus Middle	brain
27	chr16:70680400-70685600	Genic enhancers	Spleen	Spleen
28	chr16:70680600-70681000	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr16:70680600-70681000	Flanking Active TSS	HSMM	muscle
30	chr16:70680600-70681400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr16:70680600-70681600	Flanking Active TSS	HSMMtube	muscle
32	chr16:70680600-70681800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:70680600-70682000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr16:70680600-70682200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:70680800-70681000	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr16:70680800-70681000	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr16:70680800-70681000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
38	chr16:70680800-70681000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr16:70680800-70681400	Active TSS	Brain Anterior Caudate	brain
40	chr16:70680800-70681600	Enhancers	NHLF	lung
41	chr16:70680800-70683000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr16:70680800-70687800	Weak transcription	Colonic Mucosa	Colon
43	chr16:70680800-70687800	Weak transcription	Rectal Mucosa Donor 29	rectum

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