Variant report

Variant	rs16851740
Chromosome Location	chr3:141469631-141469632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141463636..141467792-chr3:141468561..141470985,4	K562	blood:
2	chr3:141467540..141469826-chr3:141482977..141484600,2	MCF-7	breast:
3	chr3:141466931..141469705-chr3:141473220..141475379,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1055690	0.82[JPT][hapmap]
rs11542226	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1533501	0.80[EUR][1000 genomes]
rs16851704	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs16851717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851752	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851763	0.88[CHB][hapmap]
rs1879284	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879285	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980192	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3773840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588340	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs57394236	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57805567	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57983026	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58115387	0.85[EUR][1000 genomes]
rs58300294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59998648	0.88[EUR][1000 genomes]
rs60938827	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61278509	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61294533	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61632965	0.88[EUR][1000 genomes]
rs6783647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73872318	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872322	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73872326	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7632069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635763	0.82[JPT][hapmap]
rs7642922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643689	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9789959	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9789973	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790069	1.00[CHB][hapmap]
rs9790073	1.00[CHB][hapmap]
rs9790075	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16851740	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141458200-141470400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:141458800-141470800	Weak transcription	Stomach Mucosa	stomach
3	chr3:141459600-141470800	Weak transcription	Fetal Brain Male	brain
4	chr3:141460200-141469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:141460400-141472400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:141460800-141470400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:141461000-141471600	Strong transcription	Fetal Thymus	thymus
8	chr3:141461200-141470000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:141461400-141470000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:141461400-141470000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:141461400-141470000	Strong transcription	Placenta	Placenta
12	chr3:141461400-141471800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:141461600-141471400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:141461800-141498200	Weak transcription	Right Ventricle	heart
15	chr3:141462000-141469800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:141462200-141470800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:141462200-141473200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:141462400-141472000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:141462600-141471400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:141462800-141470000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:141463000-141469800	Strong transcription	Adipose Nuclei	Adipose
22	chr3:141463000-141469800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:141463200-141469800	Strong transcription	Liver	Liver
24	chr3:141463200-141469800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:141463200-141470000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:141463200-141472400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:141463400-141469800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:141463400-141469800	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:141463600-141470000	Strong transcription	Fetal Intestine Large	intestine
30	chr3:141463800-141472000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:141463800-141472600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:141464600-141470000	Strong transcription	Fetal Intestine Small	intestine
33	chr3:141464600-141470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:141465000-141481400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:141465800-141472000	Strong transcription	Thymus	Thymus
36	chr3:141466000-141473000	Weak transcription	K562	blood
37	chr3:141466200-141470000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:141466200-141470600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:141466200-141471000	Weak transcription	Brain Substantia Nigra	brain
40	chr3:141466200-141471200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:141466200-141472000	Weak transcription	NHLF	lung
42	chr3:141466200-141473000	Weak transcription	NHDF-Ad	bronchial
43	chr3:141466200-141474400	Weak transcription	Primary B cells from cord blood	blood
44	chr3:141466200-141475800	Weak transcription	Psoas Muscle	Psoas
45	chr3:141466400-141470600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:141466400-141470800	Weak transcription	HSMMtube	muscle
47	chr3:141466400-141472200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:141466600-141470800	Weak transcription	Gastric	stomach
49	chr3:141466600-141472200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:141466600-141472400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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