Variant report

Variant	rs2013707
Chromosome Location	chr7:66312880-66312881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr7:66312135-66313070	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr7:66312787-66312903	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:66308321-66312999	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr7:66312833-66313002	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:66311624-66313000	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr7:66312071-66312908	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:66310807..66313244-chr7:66448820..66450934,2	MCF-7	breast:
2	chr7:66308221..66311838-chr7:66312285..66316374,5	K562	blood:
3	chr7:66312126..66314998-chr7:66385416..66387725,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCTD7-2	chr7:66312848-66312994	NONHSAT121232

No data

Variant related genes	Relation type
GTF2IRD1P1	TF binding region
ENSG00000232546	TF binding region
ENSG00000230583	Chromatin interaction
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10156059	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10224189	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10224536	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10225392	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10226191	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10229580	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10231411	0.83[EUR][1000 genomes]
rs10231860	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10234322	0.81[EUR][1000 genomes]
rs10234640	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10234747	0.85[EUR][1000 genomes]
rs10235037	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10240153	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10240582	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10241395	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10241528	0.80[EUR][1000 genomes]
rs10242870	0.83[EUR][1000 genomes]
rs10243608	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10244459	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10245017	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10247324	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10247815	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10256117	0.87[EUR][1000 genomes]
rs10258628	0.85[EUR][1000 genomes]
rs10265069	0.81[EUR][1000 genomes]
rs10265154	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10266041	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10266792	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267253	0.83[EUR][1000 genomes]
rs10270326	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10271177	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10273402	0.83[ASN][1000 genomes]
rs10280816	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10281090	0.82[EUR][1000 genomes]
rs10281544	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10282310	0.85[EUR][1000 genomes]
rs10282522	0.81[EUR][1000 genomes]
rs1060527	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1064795	0.85[EUR][1000 genomes]
rs13437994	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13438432	0.85[EUR][1000 genomes]
rs17138274	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17747927	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17748115	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1882656	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1882657	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28375318	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28379824	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28460006	0.85[EUR][1000 genomes]
rs28472679	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28501161	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28533332	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28547918	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28560293	0.81[EUR][1000 genomes]
rs28607736	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28634091	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28641990	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28663128	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28675035	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28817095	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3764904	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3778907	0.85[EUR][1000 genomes]
rs3778908	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800814	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800818	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3823607	0.81[EUR][1000 genomes]
rs3823609	0.85[EUR][1000 genomes]
rs3962133	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4718417	0.89[EUR][1000 genomes]
rs57774708	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57875851	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59079543	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59693594	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60026498	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60972148	0.89[EUR][1000 genomes]
rs61700307	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67408913	0.83[EUR][1000 genomes]
rs6964080	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6965680	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6973897	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71526586	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73133859	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73133865	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135905	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135907	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135909	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135917	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135922	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135925	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135950	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135960	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73135973	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73137960	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73137963	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73137978	0.81[ASN][1000 genomes]
rs73139941	0.81[EUR][1000 genomes]
rs73139976	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73141980	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73143921	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73143998	0.81[EUR][1000 genomes]
rs73145911	0.81[EUR][1000 genomes]
rs73145924	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73151646	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7455757	0.83[EUR][1000 genomes]
rs7777631	0.81[EUR][1000 genomes]
rs7785883	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7796977	0.82[EUR][1000 genomes]
rs7809359	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7809535	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs868960	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9654843	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv981514	chr7:66310139-66366240	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2013707	GS1-124K5.12	cis	Artery Tibial	GTEx
rs2013707	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2013707	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66310400-66337000	Weak transcription	Small Intestine	intestine
2	chr7:66310600-66313000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:66310600-66329200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:66310800-66313200	Weak transcription	NH-A	brain
5	chr7:66310800-66314600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:66310800-66324800	Weak transcription	Brain Substantia Nigra	brain
7	chr7:66310800-66331600	Weak transcription	Ovary	ovary
8	chr7:66311000-66313000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr7:66311000-66313000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr7:66311000-66313000	Weak transcription	Osteobl	bone
11	chr7:66311000-66313200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:66311000-66313200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:66311000-66313200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:66311000-66313400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:66311000-66313400	Weak transcription	A549	lung
16	chr7:66311000-66313800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr7:66311000-66314000	Weak transcription	Fetal Intestine Small	intestine
18	chr7:66311000-66322400	Weak transcription	Placenta	Placenta
19	chr7:66311000-66323400	Weak transcription	Lung	lung
20	chr7:66311000-66323600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:66311000-66323600	Weak transcription	Primary T cells from cord blood	blood
22	chr7:66311000-66324200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:66311000-66324400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:66311000-66324600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:66311000-66324600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:66311000-66324600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr7:66311000-66324600	Weak transcription	Left Ventricle	heart
28	chr7:66311000-66324600	Weak transcription	Psoas Muscle	Psoas
29	chr7:66311000-66324800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:66311000-66324800	Weak transcription	Brain Hippocampus Middle	brain
31	chr7:66311000-66324800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:66311000-66325200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr7:66311000-66329000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:66311000-66332600	Weak transcription	Colonic Mucosa	Colon
35	chr7:66311000-66339200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:66311000-66345800	Weak transcription	HSMMtube	muscle
37	chr7:66311000-66349400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:66311000-66358400	Weak transcription	Brain Anterior Caudate	brain
39	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:66311200-66313000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:66311200-66313000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr7:66311200-66313000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:66311200-66313000	Weak transcription	HMEC	breast
45	chr7:66311200-66313200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:66311200-66313200	Weak transcription	Hela-S3	cervix
47	chr7:66311200-66313200	Weak transcription	NHEK	skin
48	chr7:66311200-66322000	Weak transcription	Liver	Liver
49	chr7:66311200-66322600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:66311200-66322800	Weak transcription	Fetal Muscle Leg	muscle

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