Variant report

Variant	rs39738
Chromosome Location	chr7:30596466-30596467
allele	A/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	POLR2A	chr7:30596354-30596893	MCF10A-Er-Src	breast:	n/a	n/a
2	REST	chr7:30596097-30597126	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:30596255-30596893	H1-neurons	neurons:	n/a	n/a
4	STAT3	chr7:30596333-30597012	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr7:30596314-30597022	MCF10A-Er-Src	breast:	n/a	n/a
6	SIN3A	chr7:30596399-30596863	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr7:30596339-30596905	H1-neurons	neurons:	n/a	n/a
8	FOS	chr7:30596364-30596995	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr7:30596325-30597012	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr7:30596236-30597113	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr7:30596449-30596919	H1-hESC	embryonic stem cell:	n/a	n/a
12	FOS	chr7:30596448-30596908	MCF10A-Er-Src	breast:	n/a	n/a
13	ATF2	chr7:30596460-30596843	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:30595663..30599818-chr7:30601327..30605437,5	K562	blood:
2	chr7:30595359..30598170-chr7:30599924..30602926,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGCT-1	chr7:30587973-30601744	ENSG00000196295.7

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

Extended variants
information (count: 74 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1986756	0.82[CHB][hapmap]
rs2529437	0.82[CHB][hapmap]
rs2709790	0.86[ASN][1000 genomes]
rs2709809	0.82[CHB][hapmap]
rs28679	0.94[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38407	0.83[EUR][1000 genomes]
rs38408	0.83[EUR][1000 genomes]
rs38409	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs38410	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38411	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38413	0.80[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38414	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38415	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38416	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38417	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38418	0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38419	0.83[ASN][1000 genomes]
rs38420	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38422	0.83[ASN][1000 genomes]
rs38423	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38425	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38426	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38427	0.83[ASN][1000 genomes]
rs38429	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38430	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38432	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38433	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38434	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs38437	0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38438	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38440	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs38441	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38442	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38443	0.82[ASN][1000 genomes]
rs38444	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38445	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38446	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38447	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs38448	0.92[ASN][1000 genomes]
rs38450	0.90[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs38451	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38452	0.92[ASN][1000 genomes]
rs38453	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38454	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38455	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38456	0.93[ASN][1000 genomes]
rs38458	0.93[ASN][1000 genomes]
rs38460	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38461	0.80[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38462	0.93[ASN][1000 genomes]
rs38463	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38464	0.93[ASN][1000 genomes]
rs38465	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38466	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38468	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]
rs38469	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]
rs38471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38472	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38473	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38474	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs38478	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs38480	0.94[CEU][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38481	0.95[ASN][1000 genomes]
rs38482	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38483	0.94[ASN][1000 genomes]
rs38487	0.81[CHB][hapmap]
rs38495	0.82[CHB][hapmap]
rs40237	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4258	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]
rs4259	0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4260	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs975537	0.81[CHB][hapmap]

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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs39738	AC005154.6	cis	lung	GTEx
rs39738	AC005154.6	cis	Stomach	GTEx
rs39738	AC005154.6	cis	Muscle Skeletal	GTEx
rs39738	AC005154.8	cis	Whole Blood	GTEx
rs39738	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs39738	AC005154.6	cis	Thyroid	GTEx
rs39738	AC005154.6	cis	Esophagus Mucosa	GTEx
rs39738	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs39738	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs39738	AC005154.6	cis	Esophagus Muscularis	GTEx
rs39738	AC005154.6	cis	Whole Blood	GTEx
rs39738	AC005154.6	cis	Nerve Tibial	GTEx
rs39738	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs39738	AC005154.6	cis	Artery Tibial	GTEx
rs39738	AC005154.6	cis	Artery Aorta	GTEx

Chromatin state (count:113 , 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	chr7:30563000-30599800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:30564400-30612200	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:30569000-30602600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:30574800-30601000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr7:30575600-30600000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:30578000-30598200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:30578200-30601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:30586200-30601400	Weak transcription	Gastric	stomach
10	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
11	chr7:30587200-30602400	Weak transcription	Ovary	ovary
12	chr7:30589600-30598800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:30590000-30600400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:30590200-30602600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:30590800-30597800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr7:30591000-30599000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr7:30591000-30601400	Weak transcription	Colonic Mucosa	Colon
18	chr7:30591200-30596600	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:30591200-30598000	Weak transcription	HSMMtube	muscle
20	chr7:30591200-30598200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:30591200-30598400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:30591200-30599000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:30591200-30599800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr7:30591200-30600200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:30591200-30600200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr7:30591200-30600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:30591200-30600200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr7:30591200-30600200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr7:30591200-30600400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:30591200-30600400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:30591200-30601000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:30591200-30601000	Weak transcription	Pancreas	Pancrea
33	chr7:30591200-30602000	Weak transcription	Right Atrium	heart
34	chr7:30591200-30602600	Weak transcription	Right Ventricle	heart
35	chr7:30591200-30602600	Weak transcription	Thymus	Thymus
36	chr7:30591200-30602800	Weak transcription	Osteobl	bone
37	chr7:30591200-30604000	Weak transcription	Stomach Mucosa	stomach
38	chr7:30591200-30606200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:30591200-30610200	Weak transcription	Small Intestine	intestine
40	chr7:30591200-30612400	Weak transcription	Brain Germinal Matrix	brain
41	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
42	chr7:30591400-30603000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:30591400-30603000	Weak transcription	A549	lung
44	chr7:30591800-30599000	Weak transcription	Adipose Nuclei	Adipose
45	chr7:30591800-30600600	Weak transcription	NHDF-Ad	bronchial
46	chr7:30591800-30600800	Weak transcription	NHLF	lung
47	chr7:30591800-30601000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:30592000-30601000	Weak transcription	Hela-S3	cervix
49	chr7:30592600-30602600	Weak transcription	HepG2	liver
50	chr7:30593000-30606600	Weak transcription	Fetal Kidney	kidney

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