Variant report

Variant	rs10084280
Chromosome Location	chr2:32297984-32297985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:32225290..32227355-chr2:32297423..32299860,2	K562	blood:
2	chr2:32287760..32290675-chr2:32295373..32298097,4	K562	blood:
3	chr2:32296494..32298709-chr2:32308097..32310088,3	K562	blood:
4	chr2:32286904..32290628-chr2:32293788..32299321,9	MCF-7	breast:
5	chr2:32292512..32294326-chr2:32297664..32299959,2	K562	blood:
6	chr2:32296316..32299145-chr2:32301569..32303768,2	K562	blood:
7	chr2:32294649..32296576-chr2:32297962..32299990,3	K562	blood:

Variant related genes	Relation type
ENSG00000021574	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10084410	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169478	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10189895	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10199511	0.91[CEU][hapmap]
rs12712326	1.00[ASN][1000 genomes]
rs13425083	1.00[ASN][1000 genomes]
rs13428933	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13429391	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13431616	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011642	1.00[ASN][1000 genomes]
rs17011716	1.00[CEU][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011828	1.00[ASN][1000 genomes]
rs17011863	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs221205	1.00[ASN][1000 genomes]
rs28408351	0.83[AMR][1000 genomes]
rs28713298	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62134028	0.89[AFR][1000 genomes]
rs62142068	1.00[ASN][1000 genomes]
rs62142082	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62142083	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62142084	1.00[ASN][1000 genomes]
rs62142085	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62142088	1.00[ASN][1000 genomes]
rs62142093	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62142107	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62142443	1.00[ASN][1000 genomes]
rs62142444	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583597	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596656	0.82[AFR][1000 genomes];1.00[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	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10084280	CAPN13	cis	cerebellum	SCAN
rs10084280	DPY30	cis	parietal	SCAN
rs10084280	PLB1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32289600-32330800	Weak transcription	Spleen	Spleen
2	chr2:32289800-32298400	Weak transcription	Small Intestine	intestine
3	chr2:32289800-32304000	Weak transcription	Ovary	ovary
4	chr2:32289800-32313800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:32289800-32314600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:32289800-32315800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:32289800-32319400	Weak transcription	Aorta	Aorta
8	chr2:32289800-32319400	Weak transcription	Pancreas	Pancrea
9	chr2:32289800-32330800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:32290000-32299600	Weak transcription	Thymus	Thymus
11	chr2:32290000-32315800	Weak transcription	Fetal Kidney	kidney
12	chr2:32290000-32315800	Weak transcription	HSMM	muscle
13	chr2:32290000-32316600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:32290000-32318600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:32290200-32313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:32290200-32330800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:32290400-32298200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:32290400-32304000	Weak transcription	Adipose Nuclei	Adipose
19	chr2:32290400-32313400	Weak transcription	Fetal Thymus	thymus
20	chr2:32290400-32313800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:32290400-32315000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:32290400-32315000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:32290400-32315000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:32290400-32331000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:32290400-32353400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:32290600-32314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:32290600-32330800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:32290800-32299000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:32290800-32313600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:32290800-32313800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:32290800-32317200	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:32290800-32330200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:32291000-32298400	Weak transcription	Primary T cells from cord blood	blood
34	chr2:32291000-32299000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:32291000-32301600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:32291000-32304200	Weak transcription	GM12878-XiMat	blood
37	chr2:32291000-32314800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:32291000-32330400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:32291000-32330800	Weak transcription	Brain Angular Gyrus	brain
40	chr2:32291000-32332600	Weak transcription	A549	lung
41	chr2:32291200-32301200	Weak transcription	HMEC	breast
42	chr2:32291400-32298000	Weak transcription	HepG2	liver
43	chr2:32291400-32299000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:32291400-32327600	Weak transcription	Hela-S3	cervix
45	chr2:32291400-32331000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:32291600-32322000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:32291600-32330800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:32291600-32330800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:32291600-32332200	Weak transcription	HUVEC	blood vessel
50	chr2:32291800-32313200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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