Variant report

Variant	rs1470696
Chromosome Location	chr4:121842567-121842568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:121836736..121838271-chr4:121841875..121843483,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11723050	0.86[CHB][hapmap]
rs13149200	0.86[CHB][hapmap]
rs1376102	0.86[CHB][hapmap]
rs1450473	0.82[CHD][hapmap]
rs1588521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1901135	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2053875	0.82[CHB][hapmap]
rs2892917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3106314	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3115313	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343178	0.80[CHD][hapmap]
rs343194	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343201	0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs343202	0.81[CHD][hapmap]
rs343205	0.82[CHD][hapmap]
rs3804178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7675777	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3405799	chr4:121842552-121845050	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1470696	TNIP3	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121814600-121842600	Weak transcription	Right Ventricle	heart
2	chr4:121825000-121842600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:121837000-121842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:121837400-121842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:121838400-121842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:121838400-121842600	Weak transcription	Gastric	stomach
7	chr4:121839200-121842600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:121839200-121842600	Enhancers	Fetal Intestine Small	intestine
9	chr4:121839400-121842600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:121840000-121842600	Enhancers	Colon Smooth Muscle	Colon
11	chr4:121840000-121842600	Enhancers	Stomach Smooth Muscle	stomach
12	chr4:121840200-121842600	Weak transcription	Esophagus	oesophagus
13	chr4:121840200-121842600	Weak transcription	Left Ventricle	heart
14	chr4:121840200-121842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:121840400-121842600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:121840400-121842600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:121840400-121842600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:121840400-121842600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:121840400-121842600	Weak transcription	Small Intestine	intestine
20	chr4:121840400-121842600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:121840400-121842800	Weak transcription	Aorta	Aorta
22	chr4:121840600-121842600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:121840600-121842600	Weak transcription	Brain Substantia Nigra	brain
24	chr4:121840600-121842600	Weak transcription	Fetal Stomach	stomach
25	chr4:121840600-121842600	Weak transcription	Psoas Muscle	Psoas
26	chr4:121840600-121842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:121841000-121842600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:121841000-121842600	Weak transcription	Colonic Mucosa	Colon
29	chr4:121841000-121842600	Weak transcription	Fetal Kidney	kidney
30	chr4:121841600-121842600	Enhancers	Osteobl	bone
31	chr4:121841800-121842600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:121841800-121842600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:121841800-121842600	Weak transcription	Ovary	ovary
34	chr4:121841800-121842600	Enhancers	Hela-S3	cervix
35	chr4:121841800-121842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:121841800-121843000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr4:121841800-121843000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:121841800-121844600	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr4:121842000-121842600	Enhancers	Fetal Lung	lung
40	chr4:121842200-121842600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:121842200-121842600	Enhancers	Adipose Nuclei	Adipose
42	chr4:121842200-121842600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr4:121842200-121842800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:121842200-121842800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr4:121842200-121843000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr4:121842200-121843000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:121842400-121842600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:121842400-121842600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:121842400-121842600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:121842400-121842600	Bivalent Enhancer	Primary T cells from cord blood	blood

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