Variant report

Variant	rs742215
Chromosome Location	chr1:209961023-209961024
allele	A/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	chr1:209960927-209961266	T-47D	breast:	n/a	chr1:209961046-209961061
2	GATA3	chr1:209960932-209961397	T-47D	breast:	n/a	n/a
3	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: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044516	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11803382	0.87[EUR][1000 genomes]
rs11805830	0.87[EUR][1000 genomes]
rs12070337	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1319072	0.82[TSI][hapmap]
rs1415543	0.86[TSI][hapmap]
rs17015183	0.84[EUR][1000 genomes]
rs17015218	0.80[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17015224	0.87[EUR][1000 genomes]
rs17015226	0.80[ASW][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17015259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015309	0.91[TSI][hapmap]
rs17015379	0.82[TSI][hapmap]
rs17317411	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2013162	0.84[LWK][hapmap]
rs2073485	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073486	0.84[LWK][hapmap]
rs2235372	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235373	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235375	0.81[LWK][hapmap]
rs2236908	0.84[LWK][hapmap]
rs2236909	0.84[LWK][hapmap]
rs3753518	0.87[EUR][1000 genomes]
rs41305104	0.81[EUR][1000 genomes]
rs4556361	0.86[TSI][hapmap]
rs4844895	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58637469	0.87[EUR][1000 genomes]
rs6540559	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540560	1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6540561	0.87[EUR][1000 genomes]
rs6685182	0.84[LWK][hapmap]
rs6694552	0.87[EUR][1000 genomes]
rs6696825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742214	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522250	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525951	0.86[TSI][hapmap]
rs7539638	0.82[TSI][hapmap]
rs7545542	0.81[LWK][hapmap]
rs7550857	0.80[ASW][hapmap];0.80[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7552506	0.81[LWK][hapmap]
rs764093	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926346	0.87[EUR][1000 genomes]
rs926347	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs742215	TRAF3IP3	cis	Whole Blood	GTEx
rs742215	SYT14	cis	parietal	SCAN
rs742215	IRF6	cis	cerebellum	SCAN
rs742215	G0S2	cis	parietal	SCAN
rs742215	LPGAT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:209958200-209962600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:209958200-209963800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:209958400-209961800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:209958400-209962200	Weak transcription	Esophagus	oesophagus
8	chr1:209958400-209962200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr1:209958400-209962400	Enhancers	Stomach Mucosa	stomach
10	chr1:209958400-209962800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:209958400-209968600	Weak transcription	Lung	lung
12	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
14	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:209958600-209961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:209958600-209961400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:209958600-209961400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:209958600-209962400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:209958600-209963600	Weak transcription	HUVEC	blood vessel
20	chr1:209958600-209966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:209958600-209966600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:209958600-209967000	Genic enhancers	NHEK	skin
23	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
25	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
26	chr1:209959400-209965000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:209959600-209962200	Enhancers	Colon Smooth Muscle	Colon
28	chr1:209959600-209966000	Genic enhancers	Fetal Intestine Small	intestine
29	chr1:209959800-209962000	Genic enhancers	Fetal Intestine Large	intestine
30	chr1:209959800-209962200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:209960000-209961200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr1:209960200-209961800	Enhancers	Pancreas	Pancrea
33	chr1:209960400-209962200	Genic enhancers	HMEC	breast
34	chr1:209960400-209962600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:209960400-209963400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:209960600-209961200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr1:209960600-209961400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr1:209960600-209961400	Enhancers	Fetal Stomach	stomach
39	chr1:209960600-209961600	Flanking Active TSS	Liver	Liver
40	chr1:209960600-209961600	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr1:209960600-209961800	Weak transcription	Gastric	stomach
42	chr1:209960800-209961400	Bivalent Enhancer	Osteobl	bone
43	chr1:209960800-209962400	Weak transcription	Left Ventricle	heart
44	chr1:209960800-209963800	Weak transcription	Colonic Mucosa	Colon
45	chr1:209960800-209969000	Strong transcription	Placenta	Placenta
46	chr1:209961000-209961400	Enhancers	Fetal Heart	heart
47	chr1:209961000-209962000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:209961000-209962000	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr1:209961000-209962000	Enhancers	Rectal Smooth Muscle	rectum
50	chr1:209961000-209974600	Weak transcription	Right Atrium	heart

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