Variant report

Variant	rs4258
Chromosome Location	chr7:30589261-30589262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr7:30587837-30589288	SK-N-SH	brain:	n/a	n/a
2	SMC3	chr7:30588316-30589432	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr7:30588512-30591336	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30587105..30589528-chr7:30598413..30601345,2	K562	blood:
2	chr7:30543086..30546896-chr7:30587990..30592067,4	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30587975-30590397	ENSG00000196295.5
2	lnc-GGCT-1	chr7:30587973-30590397	NONHSAT119889
3	lnc-GGCT-1	chr7:30587975-30590397	NONHSAT119891
4	lnc-GGCT-1	chr7:30587973-30601744	ENSG00000196295.7

No data

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

Extended variants
information (count: 77 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1986756	0.82[CHB][hapmap]
rs2529437	0.82[CHB][hapmap]
rs2709790	0.81[ASN][1000 genomes]
rs2709809	0.82[CHB][hapmap]
rs28679	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38406	0.81[ASN][1000 genomes]
rs38407	0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs38408	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38409	0.81[CEU][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38410	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38411	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38413	0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38414	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38415	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38416	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38417	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38418	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38419	0.88[ASN][1000 genomes]
rs38420	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38421	0.83[ASN][1000 genomes]
rs38422	0.88[ASN][1000 genomes]
rs38423	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38425	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38426	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38427	0.88[ASN][1000 genomes]
rs38429	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38430	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38432	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38433	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38434	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38437	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38438	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38440	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38441	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38442	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38443	0.87[ASN][1000 genomes]
rs38444	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38445	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38446	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38447	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38448	0.97[ASN][1000 genomes]
rs38450	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38451	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38452	0.97[ASN][1000 genomes]
rs38453	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38454	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38455	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38456	0.99[ASN][1000 genomes]
rs38458	0.99[ASN][1000 genomes]
rs38460	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38461	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38462	0.99[ASN][1000 genomes]
rs38463	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38464	0.99[ASN][1000 genomes]
rs38465	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38466	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38472	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38473	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs38474	0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38478	0.86[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs38480	0.94[CEU][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38481	0.89[ASN][1000 genomes]
rs38482	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38483	0.89[ASN][1000 genomes]
rs38487	0.82[CHB][hapmap]
rs38495	0.82[CHB][hapmap]
rs39738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40237	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4259	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4260	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs975537	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv966770	chr7:30562144-30590529	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4258	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs4258	AC005154.6	cis	Artery Tibial	GTEx
rs4258	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs4258	AC005154.6	cis	Artery Aorta	GTEx
rs4258	AC005154.6	cis	Muscle Skeletal	GTEx
rs4258	AC005154.6	cis	Esophagus Muscularis	GTEx
rs4258	AC005154.6	cis	Esophagus Mucosa	GTEx
rs4258	AC005154.6	cis	Thyroid	GTEx
rs4258	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs4258	AC005154.6	cis	lung	GTEx
rs4258	AC005154.6	cis	Stomach	GTEx
rs4258	AC005154.6	cis	Nerve Tibial	GTEx
rs4258	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4258	AC005154.6	cis	Whole Blood	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
2	chr7:30555200-30590800	Weak transcription	Spleen	Spleen
3	chr7:30560400-30590800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:30561200-30590400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:30561200-30590600	Weak transcription	Right Ventricle	heart
6	chr7:30561600-30590600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:30563000-30599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:30564400-30590600	Weak transcription	Liver	Liver
10	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:30572400-30590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:30573000-30590400	Weak transcription	HSMM	muscle
14	chr7:30573000-30590600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:30574200-30590600	Weak transcription	GM12878-XiMat	blood
16	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:30575600-30590600	Weak transcription	Thymus	Thymus
18	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:30577000-30589400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:30577400-30589600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:30577400-30589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:30578000-30590800	Weak transcription	Placenta	Placenta
23	chr7:30578000-30598200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:30578200-30601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:30583000-30590200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr7:30583200-30590600	Weak transcription	Brain Germinal Matrix	brain
27	chr7:30583200-30590600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr7:30583600-30590200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:30584400-30590000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr7:30584400-30590400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:30584600-30590200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:30584600-30590200	Weak transcription	Osteobl	bone
33	chr7:30584600-30590600	Weak transcription	NHLF	lung
34	chr7:30584800-30589600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr7:30584800-30590600	Weak transcription	Colonic Mucosa	Colon
36	chr7:30585400-30590000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr7:30585400-30590600	Weak transcription	Pancreas	Pancrea
38	chr7:30585600-30590000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr7:30585800-30590400	Weak transcription	Fetal Heart	heart
40	chr7:30586000-30590200	Strong transcription	Primary T cells from cord blood	blood
41	chr7:30586000-30590600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:30586200-30595800	Weak transcription	Fetal Intestine Large	intestine
43	chr7:30586200-30601400	Weak transcription	Gastric	stomach
44	chr7:30586400-30590000	Strong transcription	Primary B cells from cord blood	blood
45	chr7:30586400-30590800	Weak transcription	Fetal Brain Male	brain
46	chr7:30586600-30590600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
48	chr7:30586800-30590800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:30586800-30596200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr7:30587000-30590800	Weak transcription	Fetal Muscle Trunk	muscle

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