Variant report

Variant	rs10238520
Chromosome Location	chr7:3341615-3341616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3339718..3341766-chr7:3458306..3459954,2	K562	blood:

Variant related genes	Relation type
ENSG00000211544	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10224769	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10228723	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10233166	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10250444	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10257982	0.84[ASN][1000 genomes]
rs10260145	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10261250	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10261912	0.84[ASN][1000 genomes]
rs10268249	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10276190	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10276933	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10807838	0.92[ASN][1000 genomes]
rs10951159	0.88[ASN][1000 genomes]
rs1112428	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11974620	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12537113	0.91[ASN][1000 genomes]
rs12537528	0.90[ASN][1000 genomes]
rs12537549	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540305	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12700789	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13230698	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1525556	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1525557	0.92[ASN][1000 genomes]
rs34368704	0.81[ASN][1000 genomes]
rs34608458	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34735349	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4131987	0.86[EUR][1000 genomes]
rs4255031	0.89[ASN][1000 genomes]
rs4295560	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4298408	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4316064	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4320450	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4327753	0.91[ASN][1000 genomes]
rs4336505	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4349886	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4358698	0.86[ASN][1000 genomes]
rs4385365	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4443553	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4495320	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4499989	0.90[ASN][1000 genomes]
rs4506106	0.91[ASN][1000 genomes]
rs4521670	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4544975	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4588749	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4607498	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4719883	0.92[ASN][1000 genomes]
rs4719894	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4722654	0.86[ASN][1000 genomes]
rs4722655	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4722663	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4722673	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4722674	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4722693	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4722696	0.89[ASN][1000 genomes]
rs4722708	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4722710	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4722712	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6461983	0.88[ASN][1000 genomes]
rs6461993	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6461994	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6462030	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6958390	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6959232	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6959702	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6965684	0.92[ASN][1000 genomes]
rs6966619	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6974075	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6980323	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7780027	0.80[EUR][1000 genomes]
rs7785994	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7789887	0.92[ASN][1000 genomes]
rs7791820	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7794279	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7798672	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7803993	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7811244	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9986894	0.85[ASN][1000 genomes]
rs9986896	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	esv19885	chr7:3339551-3341631	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	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
14	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
15	nsv605889	chr7:3340187-3342276	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv3421283	chr7:3340376-3342024	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	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
rs10238520	SDK1	cis	Muscle Skeletal	GTEx
rs10238520	SDK1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3339600-3342600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr7:3339800-3342200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:3339800-3342200	Active TSS	HSMMtube	muscle
4	chr7:3340000-3342200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:3340000-3342200	Active TSS	HepG2	liver
6	chr7:3340000-3342200	Active TSS	HSMM	muscle
7	chr7:3340000-3342400	Active TSS	Right Atrium	heart
8	chr7:3340000-3342600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr7:3340000-3342600	Active TSS	Rectal Smooth Muscle	rectum
10	chr7:3340000-3343400	Active TSS	Aorta	Aorta
11	chr7:3340200-3341800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:3340200-3342000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr7:3340200-3342000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:3340200-3342400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:3340200-3342400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr7:3340200-3342400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:3340200-3342400	Active TSS	Ovary	ovary
18	chr7:3340200-3342400	Active TSS	Pancreas	Pancrea
19	chr7:3340200-3342800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:3340200-3343000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr7:3340200-3343200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:3340400-3341800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:3340400-3342000	Active TSS	Gastric	stomach
24	chr7:3340400-3342200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:3340400-3342200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr7:3340400-3342200	Active TSS	Left Ventricle	heart
27	chr7:3340400-3342200	Active TSS	NH-A	brain
28	chr7:3340400-3342400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:3340400-3342400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:3340400-3342400	Active TSS	Brain Cingulate Gyrus	brain
31	chr7:3340400-3342400	Active TSS	Brain Hippocampus Middle	brain
32	chr7:3340400-3342600	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr7:3340400-3342800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr7:3340400-3343000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:3340600-3341800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr7:3340600-3341800	Active TSS	Muscle Satellite Cultured Cells	--
37	chr7:3340600-3341800	Active TSS	Spleen	Spleen
38	chr7:3340600-3342000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:3340600-3342000	Active TSS	Esophagus	oesophagus
40	chr7:3340600-3342000	Active TSS	Lung	lung
41	chr7:3340600-3342200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:3340600-3342400	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr7:3340600-3342600	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr7:3340600-3342600	Bivalent/Poised TSS	Thymus	Thymus
45	chr7:3340800-3341800	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr7:3340800-3341800	Active TSS	Small Intestine	intestine
47	chr7:3341200-3341800	Bivalent Enhancer	HMEC	breast
48	chr7:3341400-3341800	Flanking Active TSS	Psoas Muscle	Psoas
49	chr7:3341400-3341800	Bivalent/Poised TSS	NHEK	skin
50	chr7:3341400-3342000	Bivalent/Poised TSS	Fetal Intestine Small	intestine

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