Variant report

Variant	rs3778908
Chromosome Location	chr7:66255451-66255452
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	POLR2A	chr7:66254732-66255514	GM12891	blood:	n/a	n/a
2	CTCF	chr7:66255440-66255590	BJ	skin:	n/a	n/a
3	POLR2A	chr7:66255134-66255609	GM12891	blood:	n/a	n/a
4	POLR2A	chr7:66255306-66255514	HepG2	liver:	n/a	n/a
5	POLR2A	chr7:66254699-66255612	GM12878	blood:	n/a	n/a
6	MAX	chr7:66255419-66255463	NB4	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000238841	TF binding region

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10156059	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10224189	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10224536	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10225392	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10226191	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10226294	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10228381	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10229580	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10231411	0.81[AFR][1000 genomes]
rs10231860	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10234640	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10234747	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10235037	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10239200	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10240153	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10240582	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10241395	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10242870	0.81[AFR][1000 genomes]
rs10243608	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10244459	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10244602	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10245017	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10247324	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247815	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10255813	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10256117	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10258628	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10265069	0.80[AFR][1000 genomes]
rs10265154	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10266041	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10266792	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267253	0.81[AFR][1000 genomes]
rs10270326	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10271177	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10273402	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10277231	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10280717	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10280816	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10281544	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10282310	0.88[EUR][1000 genomes]
rs10282522	0.84[EUR][1000 genomes]
rs1060527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1064795	0.88[EUR][1000 genomes]
rs12333749	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13437994	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13438432	0.88[EUR][1000 genomes]
rs17138274	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17747927	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17748115	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1882656	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1882657	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2013707	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28375318	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28379824	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28460006	0.88[EUR][1000 genomes]
rs28472679	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28474923	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28501161	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28526115	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28533332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547918	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28560293	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28607736	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28634091	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28641990	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28657758	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28663128	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28675035	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3764904	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3778907	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3800814	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800818	0.84[EUR][1000 genomes]
rs3814464	0.83[ASN][1000 genomes]
rs3823607	0.84[EUR][1000 genomes]
rs3823609	0.88[EUR][1000 genomes]
rs3962133	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718417	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs57774708	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57875851	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57902746	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59079543	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59693594	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60026498	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60972148	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61700307	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6964080	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6965680	0.81[EUR][1000 genomes]
rs6973897	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73133809	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73133816	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73133859	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73133865	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135905	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135907	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135909	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135917	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135922	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135925	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135950	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135960	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73135973	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73137960	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73137963	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73137978	0.86[ASN][1000 genomes]
rs73139941	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73139976	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73141980	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73143921	0.83[EUR][1000 genomes]
rs73145924	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73151646	0.82[EUR][1000 genomes]
rs7455757	0.81[AFR][1000 genomes]
rs7785883	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7796977	0.81[AFR][1000 genomes]
rs7809359	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7809535	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9654843	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3778908	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs3778908	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs3778908	GS1-124K5.12	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
5	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr7:66236800-66276800	Strong transcription	Dnd41	blood
7	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
10	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:66238200-66276600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr7:66240400-66260000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:66242200-66260000	Weak transcription	Psoas Muscle	Psoas
14	chr7:66242400-66262600	Weak transcription	Colonic Mucosa	Colon
15	chr7:66243600-66263200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:66245600-66279200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:66245600-66279400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:66245800-66260400	Weak transcription	HUVEC	blood vessel
19	chr7:66246200-66256000	Weak transcription	Hela-S3	cervix
20	chr7:66246200-66277800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr7:66246200-66279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:66246400-66256400	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr7:66246800-66261400	Weak transcription	Esophagus	oesophagus
24	chr7:66247000-66260800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:66247600-66261000	Weak transcription	Brain Substantia Nigra	brain
26	chr7:66248400-66277800	Strong transcription	Osteobl	bone
27	chr7:66248600-66256200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:66248600-66276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:66248800-66277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr7:66249000-66256600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:66249200-66258200	Strong transcription	Placenta	Placenta
32	chr7:66249400-66278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:66249800-66256600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:66250000-66256000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:66250000-66256200	Strong transcription	Fetal Brain Female	brain
36	chr7:66250000-66258000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:66250000-66279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr7:66250000-66279200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:66250200-66255600	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr7:66250200-66255800	Strong transcription	Fetal Muscle Leg	muscle
41	chr7:66250200-66256200	Strong transcription	Fetal Intestine Large	intestine
42	chr7:66250200-66257000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:66250200-66277800	Strong transcription	Primary T cells from cord blood	blood
44	chr7:66250200-66278600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr7:66250400-66255600	Strong transcription	Fetal Intestine Small	intestine
46	chr7:66250400-66255800	Strong transcription	Fetal Stomach	stomach
47	chr7:66250400-66258000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:66250800-66255600	Strong transcription	Thymus	Thymus
49	chr7:66250800-66256200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:66250800-66256400	Strong transcription	HSMMtube	muscle

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