Variant report

Variant	rs9561866
Chromosome Location	chr13:96032829-96032830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95841276..95841834-chr13:96032679..96033583,3	K562	blood:
2	chr13:95841692..95842231-chr13:96032699..96033435,2	MCF-7	breast:
3	chr13:95843696..95844640-chr13:96032651..96033707,6	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10508012	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10508013	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1104553	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1104556	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16951044	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35218761	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4556671	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7993807	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7994250	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7995565	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7995836	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9561859	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9561860	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9561861	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9561863	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561867	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1043019	chr13:95924585-96152616	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1037673	chr13:95930191-96146554	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv541882	chr13:95930191-96146554	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039391	chr13:95931369-96038728	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv517610	chr13:95931992-96035883	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1047208	chr13:95935757-96036053	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1044162	chr13:95936858-96032829	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1040348	chr13:95939874-96032829	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1042622	chr13:95939874-96038728	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1049988	chr13:95942492-96038728	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1053262	chr13:95943731-96032829	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1047902	chr13:95945118-96032829	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv900932	chr13:95991263-96035883	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1049162	chr13:95999014-96032829	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv1047068	chr13:96000749-96032829	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv525525	chr13:96000749-96047070	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv2830243	chr13:96001349-96042020	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9561866	SOX21	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96030800-96033400	Enhancers	Liver	Liver
2	chr13:96030800-96033600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr13:96031200-96035200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:96032400-96034200	Enhancers	Fetal Stomach	stomach
5	chr13:96032600-96033000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:96032600-96033000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr13:96032600-96033000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:96032600-96033000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr13:96032600-96033000	Enhancers	Psoas Muscle	Psoas
10	chr13:96032600-96033000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr13:96032600-96033200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:96032600-96033200	Enhancers	Fetal Lung	lung
13	chr13:96032600-96033200	Enhancers	Placenta	Placenta
14	chr13:96032600-96033200	Enhancers	Ovary	ovary
15	chr13:96032600-96033200	Enhancers	Rectal Smooth Muscle	rectum
16	chr13:96032600-96033200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr13:96032600-96033400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr13:96032600-96033400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr13:96032600-96033400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:96032600-96033400	Enhancers	Fetal Muscle Leg	muscle
21	chr13:96032600-96033400	Enhancers	Stomach Mucosa	stomach
22	chr13:96032600-96033400	Enhancers	HUVEC	blood vessel
23	chr13:96032600-96033600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:96032600-96033600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr13:96032600-96033600	Enhancers	Fetal Muscle Trunk	muscle
26	chr13:96032600-96033800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr13:96032600-96033800	Enhancers	Fetal Intestine Large	intestine
28	chr13:96032600-96034000	Enhancers	GM12878-XiMat	blood
29	chr13:96032600-96034000	Enhancers	K562	blood
30	chr13:96032800-96033000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr13:96032800-96033000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:96032800-96033000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr13:96032800-96033000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr13:96032800-96033000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr13:96032800-96033000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:96032800-96033000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:96032800-96033000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr13:96032800-96033000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:96032800-96033000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:96032800-96033000	Enhancers	Brain Cingulate Gyrus	brain
41	chr13:96032800-96033000	Enhancers	Brain Hippocampus Middle	brain
42	chr13:96032800-96033000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr13:96032800-96033000	Enhancers	Brain Substantia Nigra	brain
44	chr13:96032800-96033000	Enhancers	Fetal Kidney	kidney
45	chr13:96032800-96033000	Enhancers	Right Atrium	heart
46	chr13:96032800-96033000	Flanking Active TSS	A549	lung
47	chr13:96032800-96033000	Flanking Active TSS	Hela-S3	cervix
48	chr13:96032800-96033000	Enhancers	HMEC	breast
49	chr13:96032800-96033000	Flanking Active TSS	HSMMtube	muscle
50	chr13:96032800-96033000	Flanking Active TSS	NH-A	brain

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