Variant report

Variant	rs38480
Chromosome Location	chr7:30601853-30601854
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	RAD21	chr7:30601464-30604569	SK-N-SH	brain:	n/a	chr7:30602222-30602236 chr7:30602221-30602240 chr7:30604485-30604494 chr7:30602223-30602230

Variant related genes	Relation type
ENSG00000196295	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs2709790	0.89[ASN][1000 genomes]
rs28679	0.82[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38409	0.82[CEU][hapmap]
rs38410	0.89[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38411	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38413	0.83[ASN][1000 genomes]
rs38414	0.84[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38415	0.82[ASN][1000 genomes]
rs38416	0.84[CEU][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38417	0.82[ASN][1000 genomes]
rs38418	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38419	0.82[ASN][1000 genomes]
rs38420	0.82[ASN][1000 genomes]
rs38422	0.82[ASN][1000 genomes]
rs38423	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38425	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38426	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38427	0.82[ASN][1000 genomes]
rs38429	0.85[CEU][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38430	0.82[ASN][1000 genomes]
rs38432	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38433	0.82[ASN][1000 genomes]
rs38434	0.82[ASN][1000 genomes]
rs38437	0.82[ASN][1000 genomes]
rs38438	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38440	0.81[ASN][1000 genomes]
rs38441	0.85[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38442	0.90[CEU][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38443	0.80[EUR][1000 genomes]
rs38444	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38445	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38446	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38447	0.88[ASN][1000 genomes]
rs38448	0.88[ASN][1000 genomes]
rs38450	0.88[ASN][1000 genomes]
rs38451	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38452	0.88[ASN][1000 genomes]
rs38453	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38454	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38455	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38456	0.89[ASN][1000 genomes]
rs38458	0.89[ASN][1000 genomes]
rs38460	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38461	0.89[ASN][1000 genomes]
rs38462	0.89[ASN][1000 genomes]
rs38463	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38464	0.89[ASN][1000 genomes]
rs38465	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38466	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38467	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38468	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38469	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38471	0.94[CEU][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38472	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38473	0.94[ASN][1000 genomes]
rs38474	0.95[ASN][1000 genomes]
rs38478	0.95[ASN][1000 genomes]
rs38481	0.99[ASN][1000 genomes]
rs38482	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38483	0.98[ASN][1000 genomes]
rs38487	0.82[CEU][hapmap]
rs39738	0.94[CEU][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40237	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4258	0.94[CEU][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4259	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4260	0.84[CEU][hapmap];0.84[EUR][1000 genomes];0.82[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs38480	AC005154.6	cis	Artery Aorta	GTEx
rs38480	AC005154.6	cis	Stomach	GTEx
rs38480	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38480	AC005154.6	cis	lung	GTEx
rs38480	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38480	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38480	AC005154.8	cis	Whole Blood	GTEx
rs38480	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38480	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38480	LOC401320	cis	uninvolved skin	skin_eQTL
rs38480	AC005154.6	cis	Muscle Skeletal	GTEx
rs38480	AC005154.6	cis	Artery Tibial	GTEx
rs38480	AC005154.6	cis	Nerve Tibial	GTEx
rs38480	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38480	AC005154.6	cis	Whole Blood	GTEx
rs38480	AC005154.6	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
5	chr7:30587200-30602400	Weak transcription	Ovary	ovary
6	chr7:30590200-30602600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr7:30591200-30602000	Weak transcription	Right Atrium	heart
8	chr7:30591200-30602600	Weak transcription	Right Ventricle	heart
9	chr7:30591200-30602600	Weak transcription	Thymus	Thymus
10	chr7:30591200-30602800	Weak transcription	Osteobl	bone
11	chr7:30591200-30604000	Weak transcription	Stomach Mucosa	stomach
12	chr7:30591200-30606200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr7:30591200-30610200	Weak transcription	Small Intestine	intestine
14	chr7:30591200-30612400	Weak transcription	Brain Germinal Matrix	brain
15	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
16	chr7:30591400-30603000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:30591400-30603000	Weak transcription	A549	lung
18	chr7:30592600-30602600	Weak transcription	HepG2	liver
19	chr7:30593000-30606600	Weak transcription	Fetal Kidney	kidney
20	chr7:30593800-30609400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr7:30595600-30609000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr7:30595800-30608600	Strong transcription	Placenta	Placenta
23	chr7:30595800-30608800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:30596200-30602000	Strong transcription	Fetal Stomach	stomach
25	chr7:30596200-30607200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:30596200-30608200	Strong transcription	Fetal Intestine Small	intestine
27	chr7:30596400-30603600	Strong transcription	Liver	Liver
28	chr7:30596600-30602000	Weak transcription	Fetal Brain Male	brain
29	chr7:30596600-30602000	Weak transcription	NH-A	brain
30	chr7:30596600-30602400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:30596600-30614400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:30596800-30602000	Weak transcription	Brain Angular Gyrus	brain
33	chr7:30596800-30602000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:30596800-30602000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr7:30596800-30606400	Weak transcription	Esophagus	oesophagus
36	chr7:30597000-30603600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:30597200-30603600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:30597600-30607400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr7:30597800-30602800	Weak transcription	Dnd41	blood
42	chr7:30598200-30602000	Weak transcription	Fetal Brain Female	brain
43	chr7:30598200-30602200	Weak transcription	HSMMtube	muscle
44	chr7:30598200-30604400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:30598400-30608600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr7:30598800-30602600	Enhancers	HUVEC	blood vessel
48	chr7:30598800-30603600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr7:30598800-30606200	Weak transcription	Left Ventricle	heart
50	chr7:30599400-30602000	Weak transcription	GM12878-XiMat	blood

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