Variant report

Variant	rs38438
Chromosome Location	chr7:30560395-30560396
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	CEBPB	chr7:30560122-30560779	IMR90	lung:	n/a	chr7:30560623-30560640
2	ZZZ3	chr7:30560104-30560734	GM12878	blood:	n/a	n/a
3	STAT3	chr7:30560033-30560918	MCF10A-Er-Src	breast:	n/a	chr7:30560170-30560181
4	BCLAF1	chr7:30559982-30560451	GM12878	blood:	n/a	chr7:30560172-30560181
5	SPI1	chr7:30559946-30560426	GM12878	blood:	n/a	chr7:30560172-30560181
6	POLR2A	chr7:30560393-30560705	U87	brain:	n/a	n/a
7	JUND	chr7:30560365-30560637	H1-hESC	embryonic stem cell:	n/a	chr7:30560573-30560581 chr7:30560574-30560581 chr7:30560569-30560580
8	JUND	chr7:30560392-30560658	HepG2	liver:	n/a	chr7:30560573-30560581 chr7:30560574-30560581 chr7:30560569-30560580
9	FOS	chr7:30560059-30560793	HUVEC	blood vessel:	n/a	chr7:30560251-30560261 chr7:30560251-30560261 chr7:30560573-30560581 chr7:30560574-30560581 chr7:30560569-30560580 chr7:30560252-30560260
10	SPI1	chr7:30559982-30560457	GM12891	blood:	n/a	chr7:30560172-30560181
11	STAT3	chr7:30560186-30560779	MCF10A-Er-Src	breast:	n/a	n/a
12	SPI1	chr7:30559870-30560566	GM12878	blood:	n/a	chr7:30560172-30560181
13	STAT3	chr7:30560102-30560765	MCF10A-Er-Src	breast:	n/a	chr7:30560170-30560181
14	FOS	chr7:30560091-30560765	MCF10A-Er-Src	breast:	n/a	chr7:30560251-30560261 chr7:30560251-30560261 chr7:30560573-30560581 chr7:30560574-30560581 chr7:30560569-30560580 chr7:30560252-30560260
15	FOS	chr7:30560149-30560659	MCF10A-Er-Src	breast:	n/a	chr7:30560251-30560261 chr7:30560251-30560261 chr7:30560573-30560581 chr7:30560574-30560581 chr7:30560569-30560580 chr7:30560252-30560260
16	RUNX3	chr7:30560010-30560415	GM12878	blood:	n/a	n/a
17	RUNX3	chr7:30559993-30560694	GM12878	blood:	n/a	n/a
18	CTCF	chr7:30560391-30560629	IMR90	lung:	n/a	n/a
19	FOS	chr7:30560006-30560765	MCF10A-Er-Src	breast:	n/a	chr7:30560251-30560261 chr7:30560251-30560261 chr7:30560573-30560581 chr7:30560574-30560581 chr7:30560569-30560580 chr7:30560252-30560260
20	IRF4	chr7:30559941-30560444	GM12878	blood:	n/a	n/a
21	ZZZ3	chr7:30560352-30560722	Hela-S3	cervix:	n/a	n/a
22	NFIC	chr7:30559976-30560773	GM12878	blood:	n/a	n/a
23	SPI1	chr7:30559942-30560432	GM12891	blood:	n/a	chr7:30560172-30560181

No.	Distal block	Cell Line	Cell type
1	chr7:30559848..30561674-chr7:30561797..30564564,2	K562	blood:
2	chr7:30553250..30555674-chr7:30559176..30561267,2	MCF-7	breast:
3	chr7:30559129..30562106-chr7:30564543..30567467,2	MCF-7	breast:
4	chr7:30557636..30561348-chr7:30563064..30567156,3	K562	blood:

Variant related genes	Relation type
ENSG00000264520	TF binding region
ENSG00000264520	Chromatin interaction
ENSG00000244480	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs28679	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38406	0.85[ASN][1000 genomes]
rs38407	0.90[ASN][1000 genomes]
rs38408	0.91[ASN][1000 genomes]
rs38409	0.92[ASN][1000 genomes]
rs38410	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38411	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38413	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38414	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38415	0.97[ASN][1000 genomes]
rs38416	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38417	0.97[ASN][1000 genomes]
rs38418	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38419	0.97[ASN][1000 genomes]
rs38420	0.97[ASN][1000 genomes]
rs38421	0.92[ASN][1000 genomes]
rs38422	0.97[ASN][1000 genomes]
rs38423	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38425	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38426	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38427	0.97[ASN][1000 genomes]
rs38428	0.87[ASN][1000 genomes]
rs38429	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38430	0.97[ASN][1000 genomes]
rs38432	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38433	0.97[ASN][1000 genomes]
rs38434	0.97[ASN][1000 genomes]
rs38435	0.85[ASN][1000 genomes]
rs38436	0.85[ASN][1000 genomes]
rs38437	0.97[ASN][1000 genomes]
rs38440	0.99[ASN][1000 genomes]
rs38441	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38442	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38443	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38444	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38445	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38446	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38447	0.91[ASN][1000 genomes]
rs38448	0.91[ASN][1000 genomes]
rs38450	0.91[ASN][1000 genomes]
rs38451	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38452	0.91[ASN][1000 genomes]
rs38453	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38454	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38455	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38456	0.89[ASN][1000 genomes]
rs38458	0.89[ASN][1000 genomes]
rs38460	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38461	0.89[ASN][1000 genomes]
rs38462	0.89[ASN][1000 genomes]
rs38463	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38464	0.89[ASN][1000 genomes]
rs38465	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38466	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38467	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38468	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38469	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38471	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38472	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38473	0.85[ASN][1000 genomes]
rs38474	0.84[ASN][1000 genomes]
rs38478	0.83[ASN][1000 genomes]
rs38480	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38481	0.81[ASN][1000 genomes]
rs38482	0.82[EUR][1000 genomes]
rs38483	0.80[ASN][1000 genomes]
rs39738	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40237	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4258	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4259	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4260	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs38438	AC005154.6	cis	Whole Blood	GTEx
rs38438	AC005154.6	cis	Artery Aorta	GTEx
rs38438	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38438	AC005154.6	cis	lung	GTEx
rs38438	AC005154.6	cis	Artery Tibial	GTEx
rs38438	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38438	AC005154.8	cis	Whole Blood	GTEx
rs38438	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38438	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38438	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38438	AC005154.6	cis	Nerve Tibial	GTEx
rs38438	AC005154.6	cis	Stomach	GTEx
rs38438	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38438	AC005154.6	cis	Muscle Skeletal	GTEx
rs38438	AC005154.6	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30545000-30584600	Weak transcription	Aorta	Aorta
2	chr7:30545200-30562200	Weak transcription	Small Intestine	intestine
3	chr7:30545200-30587600	Weak transcription	HSMMtube	muscle
4	chr7:30545400-30560600	Weak transcription	Brain Substantia Nigra	brain
5	chr7:30545400-30560600	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:30545400-30576200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:30545400-30576600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:30545600-30586200	Weak transcription	Brain Anterior Caudate	brain
9	chr7:30554000-30577600	Weak transcription	Placenta	Placenta
10	chr7:30554200-30560400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:30554200-30561400	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
13	chr7:30554600-30574600	Weak transcription	Primary T cells from cord blood	blood
14	chr7:30554800-30588600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr7:30555200-30590800	Weak transcription	Spleen	Spleen
16	chr7:30556800-30560600	Weak transcription	Fetal Brain Male	brain
17	chr7:30557400-30561200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:30557800-30560600	Weak transcription	Primary B cells from cord blood	blood
19	chr7:30557800-30562600	Enhancers	Fetal Intestine Small	intestine
20	chr7:30558200-30560600	Weak transcription	Colonic Mucosa	Colon
21	chr7:30558200-30568400	Enhancers	Fetal Intestine Large	intestine
22	chr7:30558800-30560400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr7:30559200-30576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:30559400-30560600	Weak transcription	Esophagus	oesophagus
25	chr7:30559600-30561800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:30559600-30562200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr7:30559800-30560600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:30559800-30561200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr7:30559800-30561200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:30559800-30561800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:30559800-30576400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:30560000-30560400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr7:30560000-30560400	Enhancers	Osteobl	bone
34	chr7:30560000-30560600	Enhancers	Primary B cells from peripheral blood	blood
35	chr7:30560000-30560800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:30560000-30560800	Weak transcription	Lung	lung
37	chr7:30560000-30561000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:30560000-30561200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr7:30560000-30561400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:30560000-30561400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:30560000-30561400	Enhancers	GM12878-XiMat	blood
42	chr7:30560000-30561600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr7:30560000-30561600	Enhancers	NHEK	skin
44	chr7:30560000-30562000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:30560000-30562200	Enhancers	NHDF-Ad	bronchial
46	chr7:30560000-30562400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr7:30560200-30560400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr7:30560200-30560400	Enhancers	K562	blood
49	chr7:30560200-30560600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr7:30560200-30560600	Enhancers	Cortex derived primary cultured neurospheres	brain

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