Variant report

Variant	rs38468
Chromosome Location	chr7:30588091-30588092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr7:30588040-30588190	GM12864	blood:	n/a	n/a
2	RAD21	chr7:30587837-30589288	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr7:30588060-30588210	BJ	skin:	n/a	n/a
4	FOXA2	chr7:30588016-30589037	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:30587105..30589528-chr7:30598413..30601345,2	K562	blood:
2	chr17:80920754..80921736-chr7:30588081..30589000,2	MCF-7	breast:
3	chr7:30586856..30589208-chr7:30590381..30593280,2	K562	blood:
4	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: 78 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs1986756	0.82[CHB][hapmap]
rs2529437	0.83[CHB][hapmap]
rs2709790	0.81[ASN][1000 genomes]
rs2709809	0.83[CHB][hapmap]
rs28679	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38406	0.81[ASN][1000 genomes]
rs38407	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs38408	0.82[ASN][1000 genomes]
rs38409	0.84[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38410	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38411	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38413	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38414	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38415	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38416	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38417	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38418	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[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	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38425	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38426	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38427	0.88[ASN][1000 genomes]
rs38429	0.90[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38430	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38432	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38433	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38434	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38437	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38438	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38440	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs38441	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38442	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38443	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38444	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38445	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38446	0.90[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	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38451	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38452	0.97[ASN][1000 genomes]
rs38453	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38454	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38455	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38456	0.99[ASN][1000 genomes]
rs38458	0.99[ASN][1000 genomes]
rs38460	0.90[AMR][1000 genomes];0.97[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	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38464	0.99[ASN][1000 genomes]
rs38465	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38466	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38472	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38473	0.91[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs38474	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38478	0.87[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs38480	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38481	0.89[ASN][1000 genomes]
rs38482	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38483	0.89[ASN][1000 genomes]
rs38487	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs38488	0.82[CHD][hapmap]
rs38495	0.82[CHB][hapmap]
rs39738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40237	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4260	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs975537	0.83[CHB][hapmap];0.82[CHD][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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs38468	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38468	CRHR2	cis	parietal	SCAN
rs38468	FKBP9	cis	parietal	SCAN
rs38468	AC005154.6	cis	Muscle Skeletal	GTEx
rs38468	AC005154.8	cis	Whole Blood	GTEx
rs38468	AC005154.6	cis	Whole Blood	GTEx
rs38468	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38468	TRIL	cis	parietal	SCAN
rs38468	AC005154.6	cis	Stomach	GTEx
rs38468	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38468	AC005154.6	cis	Artery Aorta	GTEx
rs38468	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38468	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38468	AC005154.6	cis	lung	GTEx
rs38468	AC005154.6	cis	Esophagus Mucosa	GTEx
rs38468	AC005154.6	cis	Artery Tibial	GTEx
rs38468	AC005154.6	cis	Nerve Tibial	GTEx
rs38468	AC005154.6	cis	Thyroid	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30554400-30596400	Weak transcription	Fetal Brain Female	brain
2	chr7:30554800-30588600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr7:30555200-30590800	Weak transcription	Spleen	Spleen
4	chr7:30560400-30590800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:30560600-30588200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:30560800-30588400	Weak transcription	Brain Substantia Nigra	brain
7	chr7:30561200-30590400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:30561200-30590600	Weak transcription	Right Ventricle	heart
9	chr7:30561600-30590600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:30561600-30606400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:30563000-30599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:30563600-30588800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:30564400-30590600	Weak transcription	Liver	Liver
14	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:30566000-30588600	Weak transcription	Stomach Mucosa	stomach
16	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:30571200-30588400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:30572400-30590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:30573000-30588600	Weak transcription	Psoas Muscle	Psoas
20	chr7:30573000-30590400	Weak transcription	HSMM	muscle
21	chr7:30573000-30590600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:30573800-30588400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr7:30574200-30590600	Weak transcription	GM12878-XiMat	blood
24	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:30575000-30588400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:30575200-30588400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:30575600-30590600	Weak transcription	Thymus	Thymus
28	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr7:30577000-30589400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr7:30577200-30588200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:30577400-30589600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:30577400-30589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:30578000-30590800	Weak transcription	Placenta	Placenta
34	chr7:30578000-30598200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:30578200-30601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:30579200-30588800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:30583000-30590200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr7:30583200-30590600	Weak transcription	Brain Germinal Matrix	brain
39	chr7:30583200-30590600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:30583600-30590200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:30583800-30588600	Weak transcription	K562	blood
42	chr7:30584200-30588400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:30584400-30590000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr7:30584400-30590400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr7:30584600-30588600	Weak transcription	HepG2	liver
46	chr7:30584600-30590200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:30584600-30590200	Weak transcription	Osteobl	bone
48	chr7:30584600-30590600	Weak transcription	NHLF	lung
49	chr7:30584800-30589600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr7:30584800-30590600	Weak transcription	Colonic Mucosa	Colon

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