Variant report

Variant	rs9789973
Chromosome Location	chr3:141460769-141460770
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141459822..141461407-chr3:141463215..141465670,2	MCF-7	breast:
2	chr3:141458745..141461557-chr3:141613414..141615464,2	K562	blood:
3	chr3:141459507..141461128-chr3:141567527..141569442,2	K562	blood:
4	chr3:141460404..141464291-chr3:141593804..141597029,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11542226	0.85[EUR][1000 genomes]
rs1533501	0.80[EUR][1000 genomes]
rs16851704	0.88[EUR][1000 genomes]
rs16851717	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851740	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851752	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879284	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879285	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980192	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3773840	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538350	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588340	0.80[EUR][1000 genomes]
rs57394236	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57805567	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57983026	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58115387	0.85[EUR][1000 genomes]
rs58300294	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59998648	0.88[EUR][1000 genomes]
rs60938827	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61278509	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61294533	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61632965	0.88[EUR][1000 genomes]
rs6783647	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783736	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73872318	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872319	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872322	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73872326	0.83[EUR][1000 genomes]
rs7632069	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642922	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643689	0.85[EUR][1000 genomes]
rs9789959	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9790075	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv877552	chr3:141420562-141466147	Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9789973	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141458000-141461400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:141458200-141461000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:141458200-141470400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:141458400-141463600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:141458400-141464000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:141458600-141461400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:141458600-141463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:141458600-141468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:141458800-141460800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:141458800-141461400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:141458800-141461400	Weak transcription	Right Ventricle	heart
12	chr3:141458800-141461600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:141458800-141470800	Weak transcription	Stomach Mucosa	stomach
14	chr3:141459000-141461000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:141459000-141461200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:141459000-141461400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:141459000-141461400	Weak transcription	Placenta	Placenta
18	chr3:141459000-141462000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:141459000-141462400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:141459000-141463200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:141459000-141463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:141459000-141463600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:141459000-141463600	Weak transcription	Esophagus	oesophagus
24	chr3:141459000-141465600	Weak transcription	Lung	lung
25	chr3:141459000-141465800	Weak transcription	Gastric	stomach
26	chr3:141459200-141461400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:141459400-141461400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:141459400-141464000	Weak transcription	Fetal Stomach	stomach
29	chr3:141459600-141461400	Enhancers	Pancreas	Pancrea
30	chr3:141459600-141463400	Weak transcription	Fetal Brain Female	brain
31	chr3:141459600-141464200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:141459600-141470800	Weak transcription	Fetal Brain Male	brain
33	chr3:141459800-141460800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:141459800-141461000	Genic enhancers	Fetal Thymus	thymus
35	chr3:141459800-141463400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr3:141460000-141460800	Weak transcription	Brain Substantia Nigra	brain
37	chr3:141460000-141461200	Enhancers	Colon Smooth Muscle	Colon
38	chr3:141460000-141463600	Weak transcription	Fetal Kidney	kidney
39	chr3:141460000-141467000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:141460200-141460800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:141460200-141461000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr3:141460200-141461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:141460200-141461400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:141460200-141461400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:141460200-141461400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:141460200-141461400	Weak transcription	Fetal Heart	heart
47	chr3:141460200-141461400	Weak transcription	NHDF-Ad	bronchial
48	chr3:141460200-141461600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:141460200-141461600	Weak transcription	Liver	Liver
50	chr3:141460200-141461600	Weak transcription	Brain Cingulate Gyrus	brain

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