Variant report

Variant	rs38417
Chromosome Location	chr7:30545278-30545279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:30543622-30545568	GM12891	blood:	n/a	n/a
2	POLR2A	chr7:30543934-30545466	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:30544034-30545430	K562	blood:	n/a	n/a
4	POLR2A	chr7:30543690-30545291	HL-60	blood:	n/a	n/a
5	MXI1	chr7:30541821-30545796	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr7:30543778-30545374	NB4	blood:	n/a	n/a
7	POLR2A	chr7:30543487-30545356	HepG2	liver:	n/a	n/a
8	SPI1	chr7:30544194-30545392	HL-60	blood:	n/a	chr7:30544661-30544668
9	SIN3AK20	chr7:30543626-30545340	MCF-7	breast:	n/a	n/a
10	POLR2A	chr7:30542394-30545283	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:30516309..30520214-chr7:30539829..30545899,10	MCF-7	breast:
2	chr7:30514482..30520047-chr7:30541597..30545999,6	K562	blood:
3	chr7:30543086..30546896-chr7:30587990..30592067,4	MCF-7	breast:
4	chr7:30542906..30546609-chr7:30564616..30567471,3	K562	blood:
5	chr7:30540102..30542723-chr7:30542755..30545795,4	K562	blood:
6	chr7:30537997..30542227-chr7:30542503..30545909,8	MCF-7	breast:
7	chr7:30333594..30336443-chr7:30544651..30546483,2	K562	blood:
8	chr7:30516697..30519938-chr7:30542758..30546445,6	K562	blood:
9	chr7:30516038..30518897-chr7:30540788..30545615,6	MCF-7	breast:

No data

Variant related genes	Relation type
GGCT	TF binding region
ENSG00000106100	Chromatin interaction
ENSG00000263683	Chromatin interaction
ENSG00000196295	Chromatin interaction
ENSG00000264520	Chromatin interaction
ENSG00000006625	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs2709787	0.86[EUR][1000 genomes]
rs28679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38406	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38407	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs38408	0.91[ASN][1000 genomes]
rs38409	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs38410	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38411	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38413	0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38414	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs38416	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38418	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38419	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38421	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38422	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38423	0.99[ASN][1000 genomes]
rs38425	0.99[ASN][1000 genomes]
rs38426	0.99[ASN][1000 genomes]
rs38427	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38428	0.88[ASN][1000 genomes]
rs38429	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38430	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38432	0.99[ASN][1000 genomes]
rs38433	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38434	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38435	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38436	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38438	0.97[ASN][1000 genomes]
rs38440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38441	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs38442	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs38443	0.83[ASN][1000 genomes]
rs38444	0.88[ASN][1000 genomes]
rs38445	0.89[ASN][1000 genomes]
rs38446	0.89[ASN][1000 genomes]
rs38447	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38448	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38450	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38451	0.88[ASN][1000 genomes]
rs38452	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38453	0.88[ASN][1000 genomes]
rs38454	0.88[ASN][1000 genomes]
rs38455	0.86[ASN][1000 genomes]
rs38456	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38458	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38459	0.85[EUR][1000 genomes]
rs38460	0.88[ASN][1000 genomes]
rs38461	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38462	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38463	0.88[ASN][1000 genomes]
rs38464	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38465	0.87[ASN][1000 genomes]
rs38466	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38467	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38468	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38469	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38471	0.83[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38472	0.84[ASN][1000 genomes]
rs38473	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38474	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38478	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38480	0.82[ASN][1000 genomes]
rs38481	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38483	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38485	0.87[EUR][1000 genomes]
rs38488	0.86[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs38498	0.82[EUR][1000 genomes]
rs39738	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs40237	0.99[ASN][1000 genomes]
rs4258	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4260	0.91[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs973002	0.89[TSI][hapmap]

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs38417	AC005154.6	cis	Muscle Skeletal	GTEx
rs38417	AC005154.6	cis	Nerve Tibial	GTEx
rs38417	AC005154.6	cis	lung	GTEx
rs38417	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38417	AC005154.8	cis	Whole Blood	GTEx
rs38417	AC005154.6	cis	Thyroid	GTEx
rs38417	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38417	AC005154.6	cis	Artery Aorta	GTEx
rs38417	AC005154.8	cis	lung	GTEx
rs38417	AC005154.6	cis	Stomach	GTEx
rs38417	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38417	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38417	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38417	AC005154.6	cis	Artery Tibial	GTEx
rs38417	PRR15	cis	cerebellum	SCAN
rs38417	AC005154.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30542400-30545600	Active TSS	NHLF	lung
2	chr7:30543200-30545400	Active TSS	A549	lung
3	chr7:30543400-30545600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:30543600-30545400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:30543600-30545400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:30543800-30545400	Active TSS	Brain Hippocampus Middle	brain
7	chr7:30543800-30545600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:30544200-30545400	Active TSS	Stomach Smooth Muscle	stomach
9	chr7:30544800-30545400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:30544800-30545400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr7:30544800-30545400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:30544800-30545400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:30544800-30545400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:30544800-30545400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:30544800-30545400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr7:30544800-30545400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr7:30544800-30545400	Flanking Active TSS	Dnd41	blood
18	chr7:30544800-30545400	Flanking Active TSS	GM12878-XiMat	blood
19	chr7:30544800-30545400	Flanking Active TSS	HMEC	breast
20	chr7:30544800-30545400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr7:30545000-30545400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr7:30545000-30545400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr7:30545000-30545400	Flanking Active TSS	Liver	Liver
24	chr7:30545000-30545400	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr7:30545000-30545400	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr7:30545000-30545400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr7:30545000-30545400	Flanking Active TSS	Right Ventricle	heart
28	chr7:30545000-30545400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr7:30545000-30545400	Flanking Active TSS	NHEK	skin
30	chr7:30545000-30545400	Flanking Active TSS	Osteobl	bone
31	chr7:30545000-30545600	Flanking Active TSS	K562	blood
32	chr7:30545000-30548800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr7:30545000-30584600	Weak transcription	Aorta	Aorta
34	chr7:30545200-30545400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:30545200-30545400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr7:30545200-30545400	Enhancers	Primary B cells from cord blood	blood
37	chr7:30545200-30545400	Enhancers	Primary B cells from peripheral blood	blood
38	chr7:30545200-30545400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr7:30545200-30545400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr7:30545200-30545400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr7:30545200-30545400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr7:30545200-30545400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr7:30545200-30545400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr7:30545200-30545400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:30545200-30545400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:30545200-30545400	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr7:30545200-30545400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:30545200-30545400	Enhancers	Brain Substantia Nigra	brain
49	chr7:30545200-30545400	Enhancers	Fetal Heart	heart
50	chr7:30545200-30545400	Enhancers	Fetal Intestine Large	intestine

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