Variant report

Variant	rs4975269
Chromosome Location	chr4:129752134-129752135
allele	G/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	RELA	chr4:129751938-129754356	GM18951	blood:	n/a	n/a
2	RUNX3	chr4:129751833-129752478	GM12878	blood:	n/a	n/a
3	BHLHE40	chr4:129752130-129752573	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:129751812-129753954	GM12891	blood:	n/a	n/a
5	POLR2A	chr4:129751847-129752654	H1-hESC	embryonic stem cell:	n/a	n/a
6	EBF1	chr4:129751978-129752703	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:129751584-129753214	H1-hESC	embryonic stem cell:	n/a	n/a
8	WRNIP1	chr4:129752049-129752627	GM12878	blood:	n/a	n/a
9	RELA	chr4:129751922-129753648	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
JADE1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10008927	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10032000	1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs12512715	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120702	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13143771	0.85[CHD][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs1668289	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1841259	0.82[ASN][1000 genomes]
rs1841260	0.84[ASN][1000 genomes]
rs2016294	0.82[JPT][hapmap]
rs2162126	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217023	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099899	0.81[JPT][hapmap]
rs3113407	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs318500	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318501	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318502	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318503	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318513	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs318517	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318521	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318536	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs318543	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap]
rs318552	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4975265	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975267	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975270	0.82[JPT][hapmap]
rs4975274	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62317870	0.84[ASN][1000 genomes]
rs6817004	0.82[ASN][1000 genomes]
rs6834108	0.82[ASN][1000 genomes]
rs6847753	0.88[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs6857659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687562	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4975269	SCLT1	cis	cerebellum	SCAN
rs4975269	C4orf33	cis	Artery Tibial	GTEx
rs4975269	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs4975269	C4orf33	cis	multi-tissue	Pritchard
rs4975269	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs4975269	C4orf33	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
2	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
3	chr4:129746600-129752800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:129746600-129761800	Strong transcription	Dnd41	blood
5	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:129746800-129770200	Weak transcription	HMEC	breast
7	chr4:129747000-129752200	Weak transcription	Hela-S3	cervix
8	chr4:129747000-129766600	Weak transcription	NHEK	skin
9	chr4:129747400-129752200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:129747400-129752200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:129747400-129752400	Weak transcription	HSMMtube	muscle
12	chr4:129747400-129754200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
14	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
15	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:129749000-129754200	Genic enhancers	H1 Cell Line	embryonic stem cell
17	chr4:129749600-129752400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr4:129749600-129752400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:129750000-129753200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:129751000-129752400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr4:129751400-129752200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:129751400-129752600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr4:129751400-129752600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:129751400-129752800	Enhancers	Lung	lung
25	chr4:129751400-129753400	Enhancers	Psoas Muscle	Psoas
26	chr4:129751400-129753600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr4:129751600-129752200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:129751600-129752200	Enhancers	Right Atrium	heart
29	chr4:129751600-129752200	Enhancers	Spleen	Spleen
30	chr4:129751600-129752400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:129751600-129752400	Enhancers	Brain Anterior Caudate	brain
32	chr4:129751600-129752400	Enhancers	HepG2	liver
33	chr4:129751600-129752600	Flanking Active TSS	GM12878-XiMat	blood
34	chr4:129751600-129752800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr4:129751600-129753000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:129751600-129753000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:129751600-129753000	Enhancers	Primary B cells from peripheral blood	blood
38	chr4:129751600-129753000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr4:129751600-129753000	Genic enhancers	Thymus	Thymus
40	chr4:129751600-129753200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:129751600-129753200	Enhancers	Adipose Nuclei	Adipose
42	chr4:129751600-129753200	Enhancers	Gastric	stomach
43	chr4:129751600-129753200	Enhancers	Left Ventricle	heart
44	chr4:129751600-129753200	Enhancers	Ovary	ovary
45	chr4:129751600-129753200	Genic enhancers	K562	blood
46	chr4:129751600-129753400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr4:129751600-129753400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr4:129751600-129753400	Enhancers	Right Ventricle	heart
49	chr4:129751600-129753400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr4:129751600-129753600	Enhancers	Stomach Mucosa	stomach

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