Variant report

Variant	rs16851717
Chromosome Location	chr3:141462748-141462749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:141462090-141462767	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141460791..141464587-chr3:141594120..141597016,3	MCF-7	breast:
2	chr3:141460404..141464291-chr3:141593804..141597029,4	MCF-7	breast:

Variant related genes	Relation type
RNF7	TF binding region
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 40 )
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]
rs16851740	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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851763	0.88[CHB][hapmap]
rs1879284	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980192	0.84[AFR][1000 genomes];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];0.95[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];0.89[AFR][1000 genomes];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	0.95[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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59998648	0.88[EUR][1000 genomes]
rs60938827	0.95[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783736	0.95[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635763	0.82[JPT][hapmap]
rs7642922	0.95[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	0.95[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: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
rs16851717	RNF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr3:141458400-141463600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:141458400-141464000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:141458600-141463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:141458600-141468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:141458800-141470800	Weak transcription	Stomach Mucosa	stomach
7	chr3:141459000-141463200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:141459000-141463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:141459000-141463600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:141459000-141463600	Weak transcription	Esophagus	oesophagus
11	chr3:141459000-141465600	Weak transcription	Lung	lung
12	chr3:141459000-141465800	Weak transcription	Gastric	stomach
13	chr3:141459400-141464000	Weak transcription	Fetal Stomach	stomach
14	chr3:141459600-141463400	Weak transcription	Fetal Brain Female	brain
15	chr3:141459600-141464200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:141459600-141470800	Weak transcription	Fetal Brain Male	brain
17	chr3:141459800-141463400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:141460000-141463600	Weak transcription	Fetal Kidney	kidney
19	chr3:141460000-141467000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:141460200-141463200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr3:141460200-141463400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:141460200-141463400	Weak transcription	Thymus	Thymus
23	chr3:141460200-141463400	Weak transcription	HMEC	breast
24	chr3:141460200-141463600	Weak transcription	Colonic Mucosa	Colon
25	chr3:141460200-141464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:141460200-141464000	Weak transcription	HSMMtube	muscle
27	chr3:141460200-141466000	Weak transcription	Ovary	ovary
28	chr3:141460200-141466400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:141460200-141468000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:141460200-141468200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:141460200-141469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:141460400-141463000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:141460400-141463000	Weak transcription	Adipose Nuclei	Adipose
34	chr3:141460400-141463200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:141460400-141463200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:141460400-141463200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:141460400-141463400	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:141460400-141463400	Weak transcription	Left Ventricle	heart
39	chr3:141460400-141463400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:141460400-141463400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:141460400-141463600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr3:141460400-141463800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:141460400-141464000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:141460400-141464000	Weak transcription	Spleen	Spleen
45	chr3:141460400-141465800	Weak transcription	Aorta	Aorta
46	chr3:141460400-141465800	Weak transcription	Psoas Muscle	Psoas
47	chr3:141460400-141466000	Weak transcription	Small Intestine	intestine
48	chr3:141460400-141472400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:141460600-141462800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:141460600-141463000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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