Variant report

Variant	rs7798672
Chromosome Location	chr7:3342334-3342335
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	RAD21	chr7:3341801-3342355	MCF-7	breast:	n/a	n/a
2	RAD21	chr7:3341823-3342376	MCF-7	breast:	n/a	n/a
3	CTCF	chr7:3341403-3342389	A549	lung:	n/a	n/a
4	CTCF	chr7:3341858-3342364	MCF-7	breast:	n/a	n/a
5	TCF7L2	chr7:3342190-3343032	HEK293	kidney:	n/a	n/a
6	CTCF	chr7:3341851-3342396	MCF-7	breast:	n/a	n/a
7	RAD21	chr7:3341429-3344236	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236708	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10224769	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10228723	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10233166	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10238520	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10250444	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10257982	0.89[ASN][1000 genomes]
rs10260145	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10261250	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10261912	0.89[ASN][1000 genomes]
rs10268249	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10276190	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10276933	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10807838	0.97[ASN][1000 genomes]
rs10951155	0.83[ASN][1000 genomes]
rs10951159	0.93[ASN][1000 genomes]
rs1112428	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11974620	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537113	0.97[ASN][1000 genomes]
rs12537528	0.95[ASN][1000 genomes]
rs12537549	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12540305	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12700789	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13230698	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525556	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525557	0.97[ASN][1000 genomes]
rs34608458	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34735349	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4131987	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4255031	0.94[ASN][1000 genomes]
rs4295560	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4298408	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4316064	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4320450	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4327753	0.97[ASN][1000 genomes]
rs4336505	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4349886	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4358698	0.91[ASN][1000 genomes]
rs4385365	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4443553	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4495320	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4499989	0.95[ASN][1000 genomes]
rs4506106	0.97[ASN][1000 genomes]
rs4521670	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4544975	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4588749	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4607498	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4719883	0.97[ASN][1000 genomes]
rs4719894	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722654	0.91[ASN][1000 genomes]
rs4722655	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4722663	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722673	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722674	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722693	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4722696	0.94[ASN][1000 genomes]
rs4722708	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4722709	0.81[ASN][1000 genomes]
rs4722710	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4722712	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6461983	0.94[ASN][1000 genomes]
rs6461993	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461994	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6462030	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6651070	0.80[AMR][1000 genomes]
rs67586312	0.81[ASN][1000 genomes]
rs6958390	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6959232	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6959702	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6965684	0.97[ASN][1000 genomes]
rs6966619	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6974075	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6980323	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7780027	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7785994	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789887	0.98[ASN][1000 genomes]
rs7791820	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7798418	0.81[ASN][1000 genomes]
rs7803993	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7811244	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7811286	0.83[ASN][1000 genomes]
rs9986894	0.90[ASN][1000 genomes]
rs9986896	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464264	chr7:3194156-3349625	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv605880	chr7:3194156-3349625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3328363	chr7:3339726-3342349	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv3345863	chr7:3339851-3342399	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7798672	SDK1	cis	Muscle Skeletal	GTEx
rs7798672	SDK1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3339600-3342600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:3340000-3342400	Active TSS	Right Atrium	heart
3	chr7:3340000-3342600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr7:3340000-3342600	Active TSS	Rectal Smooth Muscle	rectum
5	chr7:3340000-3343400	Active TSS	Aorta	Aorta
6	chr7:3340200-3342400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:3340200-3342400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr7:3340200-3342400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:3340200-3342400	Active TSS	Ovary	ovary
10	chr7:3340200-3342400	Active TSS	Pancreas	Pancrea
11	chr7:3340200-3342800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:3340200-3343000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:3340200-3343200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:3340400-3342400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:3340400-3342400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:3340400-3342400	Active TSS	Brain Cingulate Gyrus	brain
17	chr7:3340400-3342400	Active TSS	Brain Hippocampus Middle	brain
18	chr7:3340400-3342600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr7:3340400-3342800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr7:3340400-3343000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:3340600-3342400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr7:3340600-3342600	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr7:3340600-3342600	Bivalent/Poised TSS	Thymus	Thymus
24	chr7:3341400-3342400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:3341400-3342400	Active TSS	Brain Anterior Caudate	brain
26	chr7:3341400-3342400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:3341400-3342400	Active TSS	Brain Substantia Nigra	brain
28	chr7:3341400-3342600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr7:3341400-3342600	Active TSS	Colon Smooth Muscle	Colon
30	chr7:3341400-3342600	Active TSS	Fetal Intestine Large	intestine
31	chr7:3341400-3342800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr7:3341400-3342800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr7:3341600-3342400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:3341600-3342400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:3341600-3342400	Active TSS	Fetal Kidney	kidney
36	chr7:3341600-3342400	Active TSS	Fetal Lung	lung
37	chr7:3341600-3342400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr7:3341600-3342600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr7:3341600-3342600	Bivalent/Poised TSS	NHLF	lung
40	chr7:3341600-3342800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr7:3341600-3342800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
42	chr7:3341600-3342800	Bivalent/Poised TSS	NHDF-Ad	bronchial
43	chr7:3341800-3342600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr7:3342000-3342400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr7:3342000-3342400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:3342000-3342400	Active TSS	Fetal Intestine Small	intestine
47	chr7:3342000-3342400	Enhancers	Placenta	Placenta
48	chr7:3342000-3342600	Flanking Active TSS	Fetal Heart	heart
49	chr7:3342000-3342600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
50	chr7:3342000-3342600	Active TSS	Right Ventricle	heart

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