Variant report

Variant	rs38469
Chromosome Location	chr7:30588609-30588610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:230)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:230 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr7:30588540-30588690	GM06990	blood:	n/a	n/a
2	MYC	chr7:30588445-30588699	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr7:30588480-30588630	HPF	lung:	n/a	n/a
4	CTCF	chr7:30588476-30588685	A549	lung:	n/a	n/a
5	RAD21	chr7:30588392-30588690	K562	blood:	n/a	n/a
6	CTCF	chr7:30588480-30588630	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr7:30588520-30588670	GM12867	blood:	n/a	n/a
8	STAT3	chr7:30588524-30588704	MCF10A-Er-Src	breast:	n/a	n/a
9	WRNIP1	chr7:30588448-30588647	GM12878	blood:	n/a	n/a
10	FOXA1	chr7:30588451-30588669	ECC-1	luminal epithelium:	n/a	chr7:30588578-30588593
11	CTCF	chr7:30588372-30588708	K562	blood:	n/a	n/a
12	CTCF	chr7:30588500-30588650	HCFaa	heart:	n/a	n/a
13	CTCF	chr7:30588500-30588650	HMF	breast:	n/a	n/a
14	CTCF	chr7:30588382-30588907	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr7:30588540-30588690	GM12865	blood:	n/a	n/a
16	CTCF	chr7:30588442-30588699	LNCaP	prostate:	n/a	n/a
17	CTCF	chr7:30588158-30588994	HCT-116	colon:	n/a	n/a
18	RAD21	chr7:30588397-30588749	K562	blood:	n/a	n/a
19	RAD21	chr7:30588393-30588728	A549	lung:	n/a	n/a
20	CTCF	chr7:30588520-30588670	BE2_C	brain:	n/a	n/a
21	CTCF	chr7:30588520-30588670	GM12872	blood:	n/a	n/a
22	RAD21	chr7:30588269-30588876	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr7:30588540-30588690	AG10803	skin:	n/a	n/a
24	CTCF	chr7:30588480-30588630	GM12872	blood:	n/a	n/a
25	CTCF	chr7:30588369-30588799	IMR90	lung:	n/a	n/a
26	CTCF	chr7:30588409-30588826	MCF-7	breast:	n/a	n/a
27	CTCF	chr7:30588375-30588702	SK-N-SH_RA	brain:	n/a	n/a
28	CTCF	chr7:30588520-30588670	NHDF-neo	bronchial:	n/a	n/a
29	CTCF	chr7:30588480-30588630	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr7:30588480-30588630	A549	lung:	n/a	n/a
31	CTCF	chr7:30588520-30588670	HRPEpiC	eye:	n/a	n/a
32	RAD21	chr7:30588387-30588816	GM12878	blood:	n/a	n/a
33	FOXA2	chr7:30588396-30588898	A549	lung:	n/a	n/a
34	CTCF	chr7:30588580-30588730	HFF-Myc	foreskin:	n/a	n/a
35	CTCF	chr7:30588460-30588655	GM20000	blood:	n/a	n/a
36	CTCF	chr7:30588453-30588680	MCF-7	breast:	n/a	n/a
37	FOXA2	chr7:30588430-30588862	A549	lung:	n/a	n/a
38	ARID3A	chr7:30588467-30588684	K562	blood:	n/a	n/a
39	CTCF	chr7:30588392-30588704	HepG2	liver:	n/a	n/a
40	CTCF	chr7:30588453-30588672	MCF-7	breast:	n/a	n/a
41	CTCF	chr7:30588500-30588650	WERI-Rb-1	eye:	n/a	n/a
42	CTCF	chr7:30588461-30588674	GM13976	blood:	n/a	n/a
43	CTCF	chr7:30588520-30588670	GM12868	blood:	n/a	n/a
44	CTCF	chr7:30588540-30588690	WI-38	lung:	n/a	n/a
45	CTCF	chr7:30588430-30588706	Lung_OC	lung:	n/a	n/a
46	CTCF	chr7:30588520-30588670	HEEpiC	esophagus:	n/a	n/a
47	FOXA1	chr7:30588328-30588855	HepG2	liver:	n/a	chr7:30588578-30588593
48	RAD21	chr7:30588338-30588911	HCT-116	colon:	n/a	n/a
49	CTCF	chr7:30588439-30588678	HepG2	liver:	n/a	n/a
50	CTCF	chr7:30588540-30588690	GM12868	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:30588489..30589128-chr7:30603528..30604443,5	MCF-7	breast:
2	chr7:30588102..30589045-chr7:30603634..30604619,3	K562	blood:
3	chr7:30587105..30589528-chr7:30598413..30601345,2	K562	blood:
4	chr17:80920754..80921736-chr7:30588081..30589000,2	MCF-7	breast:
5	chr7:30588178..30589001-chr7:30603651..30604516,2	MCF-7	breast:
6	chr7:30586856..30589208-chr7:30590381..30593280,2	K562	blood:
7	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
ENSG00000196295	Chromatin interaction
ENSG00000006625	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1986756	0.83[CHB][hapmap]
rs2529437	0.83[CHB][hapmap]
rs2709790	0.81[ASN][1000 genomes]
rs2709809	0.83[CHB][hapmap]
rs28679	0.89[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	0.84[CEU][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs38410	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38411	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38413	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38414	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38415	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38416	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38417	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38418	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38419	0.88[ASN][1000 genomes]
rs38420	0.83[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	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38430	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38432	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38433	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38434	0.83[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs38437	0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38438	0.83[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];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38442	0.90[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	0.91[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	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38454	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38455	0.94[AFR][1000 genomes];0.95[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	0.84[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	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38466	0.85[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];0.83[AFR][1000 genomes];0.89[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];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38473	0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs38474	0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38478	0.87[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs38480	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38481	0.89[ASN][1000 genomes]
rs38482	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38483	0.89[ASN][1000 genomes]
rs38487	0.83[CHB][hapmap]
rs38495	0.83[CHB][hapmap]
rs39738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40237	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4258	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]
rs4259	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4260	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs975537	0.83[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs38469	AC005154.6	cis	Nerve Tibial	GTEx
rs38469	AC005154.6	cis	Thyroid	GTEx
rs38469	AC005154.6	cis	lung	GTEx
rs38469	AC005154.6	cis	Stomach	GTEx
rs38469	AC005154.8	cis	Whole Blood	GTEx
rs38469	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs38469	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs38469	AC005154.6	cis	Artery Tibial	GTEx
rs38469	AC005154.6	cis	Artery Aorta	GTEx
rs38469	AC005154.6	cis	Muscle Skeletal	GTEx
rs38469	AC005154.6	cis	Whole Blood	GTEx
rs38469	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs38469	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs38469	AC005154.6	cis	Esophagus Muscularis	GTEx
rs38469	AC005154.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:107 , 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	chr7:30563600-30588800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:30564400-30590600	Weak transcription	Liver	Liver
11	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:30572400-30590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:30573000-30590400	Weak transcription	HSMM	muscle
15	chr7:30573000-30590600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:30574200-30590600	Weak transcription	GM12878-XiMat	blood
17	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:30575600-30590600	Weak transcription	Thymus	Thymus
19	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:30577000-30589400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:30577400-30589600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:30577400-30589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:30578000-30590800	Weak transcription	Placenta	Placenta
24	chr7:30578000-30598200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:30578200-30601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:30579200-30588800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:30583000-30590200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:30583200-30590600	Weak transcription	Brain Germinal Matrix	brain
29	chr7:30583200-30590600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr7:30583600-30590200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:30584400-30590000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:30584400-30590400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:30584600-30590200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:30584600-30590200	Weak transcription	Osteobl	bone
35	chr7:30584600-30590600	Weak transcription	NHLF	lung
36	chr7:30584800-30589600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr7:30584800-30590600	Weak transcription	Colonic Mucosa	Colon
38	chr7:30585400-30590000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr7:30585400-30590600	Weak transcription	Pancreas	Pancrea
40	chr7:30585600-30590000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr7:30585800-30590400	Weak transcription	Fetal Heart	heart
42	chr7:30586000-30590200	Strong transcription	Primary T cells from cord blood	blood
43	chr7:30586000-30590600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:30586200-30588800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:30586200-30595800	Weak transcription	Fetal Intestine Large	intestine
46	chr7:30586200-30601400	Weak transcription	Gastric	stomach
47	chr7:30586400-30590000	Strong transcription	Primary B cells from cord blood	blood
48	chr7:30586400-30590800	Weak transcription	Fetal Brain Male	brain
49	chr7:30586600-30590600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus

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