Variant report

Variant	rs742214
Chromosome Location	chr1:209960925-209960926
allele	C/T
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	FOXA1	chr1:209960902-209961265	T-47D	breast:	n/a	chr1:209961046-209961061

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209955520..209962214-chr1:209976009..209982555,8	K562	blood:
2	chr1:209958606..209961246-chr1:209973550..209976119,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf74-1	chr1:209960924-209961038	ENSG00000232222.1

Variant related genes	Relation type
C1orf74	TF binding region
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1044516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11803382	0.87[EUR][1000 genomes]
rs11805830	0.87[EUR][1000 genomes]
rs12070337	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015183	0.84[EUR][1000 genomes]
rs17015218	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17015224	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17015226	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17015259	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17317411	0.82[EUR][1000 genomes]
rs2073485	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235373	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753518	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs41305104	0.81[EUR][1000 genomes]
rs4844895	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58637469	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6540559	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540560	0.87[EUR][1000 genomes]
rs6540561	0.87[EUR][1000 genomes]
rs6694552	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6696825	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742215	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522250	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550857	0.87[EUR][1000 genomes]
rs764093	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926346	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs926347	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs742214	TRAF3IP3	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209961000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:209958000-209961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:209958200-209962600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:209958200-209963800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:209958400-209961800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:209958400-209962200	Weak transcription	Esophagus	oesophagus
9	chr1:209958400-209962200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr1:209958400-209962400	Enhancers	Stomach Mucosa	stomach
11	chr1:209958400-209962800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:209958400-209968600	Weak transcription	Lung	lung
13	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
15	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:209958600-209961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:209958600-209961400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:209958600-209961400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:209958600-209962400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:209958600-209963600	Weak transcription	HUVEC	blood vessel
21	chr1:209958600-209966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:209958600-209966600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:209958600-209967000	Genic enhancers	NHEK	skin
24	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
26	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
27	chr1:209959400-209965000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:209959600-209962200	Enhancers	Colon Smooth Muscle	Colon
29	chr1:209959600-209966000	Genic enhancers	Fetal Intestine Small	intestine
30	chr1:209959800-209961000	Enhancers	Adipose Nuclei	Adipose
31	chr1:209959800-209962000	Genic enhancers	Fetal Intestine Large	intestine
32	chr1:209959800-209962200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:209960000-209961200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:209960200-209961000	Enhancers	Right Atrium	heart
35	chr1:209960200-209961800	Enhancers	Pancreas	Pancrea
36	chr1:209960400-209962200	Genic enhancers	HMEC	breast
37	chr1:209960400-209962600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:209960400-209963400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:209960600-209961000	Bivalent Enhancer	Fetal Lung	lung
40	chr1:209960600-209961000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
41	chr1:209960600-209961000	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr1:209960600-209961200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:209960600-209961400	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr1:209960600-209961400	Enhancers	Fetal Stomach	stomach
45	chr1:209960600-209961600	Flanking Active TSS	Liver	Liver
46	chr1:209960600-209961600	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr1:209960600-209961800	Weak transcription	Gastric	stomach
48	chr1:209960800-209961000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:209960800-209961000	Flanking Active TSS	Fetal Heart	heart
50	chr1:209960800-209961400	Bivalent Enhancer	Osteobl	bone

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