Variant report

Variant	rs2837015
Chromosome Location	chr21:40786415-40786416
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40758859..40762254-chr21:40785710..40788224,3	MCF-7	breast:
2	chr21:40784167..40788125-chr21:40789270..40793629,5	K562	blood:
3	chr21:40784172..40786571-chr21:40796585..40798717,2	K562	blood:
4	chr21:40785010..40786571-chr21:40794751..40798085,3	K562	blood:
5	chr21:40784043..40786943-chr21:40818304..40821060,2	K562	blood:
6	chr21:40783103..40784656-chr21:40785669..40787209,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11575939	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16997618	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2065313	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2205200	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2205201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2223028	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2246078	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2410128	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837009	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837018	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2837019	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837020	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2837021	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2837023	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837024	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837026	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837029	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837031	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837032	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837034	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837037	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837039	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837040	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2840267	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4281987	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56812456	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56866897	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58265345	0.89[ASN][1000 genomes]
rs58900137	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs596289	1.00[JPT][hapmap]
rs61342945	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7275686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276981	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7277627	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7279753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73365952	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73367928	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367958	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367962	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367974	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73367976	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906032	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906033	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906034	1.00[ASN][1000 genomes]
rs940625	1.00[JPT][hapmap]
rs9680443	0.84[EUR][1000 genomes];0.81[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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3355532	chr21:40783721-40786949	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2837015	LCA5L	cis	Artery Tibial	GTEx
rs2837015	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2837015	SH3BGR	cis	Adipose Subcutaneous	GTEx
rs2837015	WRB	cis	Adipose Subcutaneous	GTEx
rs2837015	WRB	cis	Nerve Tibial	GTEx
rs2837015	WRB	cis	lung	GTEx
rs2837015	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2837015	LCA5L	cis	Thyroid	GTEx
rs2837015	LCA5L	cis	Nerve Tibial	GTEx
rs2837015	LCA5L	cis	lung	GTEx
rs2837015	WRB	cis	Artery Tibial	GTEx
rs2837015	WRB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40764600-40800600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
3	chr21:40778400-40787200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr21:40778400-40787200	Weak transcription	NHEK	skin
5	chr21:40778400-40787400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr21:40778400-40787400	Weak transcription	HSMM	muscle
7	chr21:40778400-40787800	Weak transcription	Spleen	Spleen
8	chr21:40778400-40788200	Weak transcription	Fetal Brain Male	brain
9	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
10	chr21:40779200-40788800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr21:40779200-40801400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:40779800-40794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:40779800-40794200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr21:40780200-40791000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr21:40780400-40802200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:40780600-40786800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr21:40780600-40787400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr21:40780600-40787800	Weak transcription	Adipose Nuclei	Adipose
19	chr21:40780600-40787800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr21:40780600-40789800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr21:40780600-40790000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr21:40780600-40790600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr21:40780600-40794200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:40780600-40801800	Weak transcription	Lung	lung
25	chr21:40780800-40787400	Weak transcription	Fetal Brain Female	brain
26	chr21:40780800-40787400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr21:40780800-40789200	Weak transcription	Fetal Intestine Small	intestine
28	chr21:40780800-40791800	Weak transcription	Brain Substantia Nigra	brain
29	chr21:40780800-40794200	Weak transcription	Brain Germinal Matrix	brain
30	chr21:40781000-40788000	Weak transcription	Primary T cells from cord blood	blood
31	chr21:40781000-40788000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr21:40781200-40787600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr21:40781200-40787800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr21:40781200-40798600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr21:40781200-40811000	Weak transcription	Aorta	Aorta
36	chr21:40781200-40813000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr21:40781200-40813200	Weak transcription	HSMMtube	muscle
38	chr21:40781400-40787600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:40781400-40787600	Weak transcription	Fetal Muscle Leg	muscle
40	chr21:40781400-40802000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr21:40784400-40786600	Strong transcription	Ovary	ovary
42	chr21:40785000-40800600	Weak transcription	Gastric	stomach
43	chr21:40786200-40786600	Enhancers	K562	blood
44	chr21:40786200-40787800	Weak transcription	Right Ventricle	heart
45	chr21:40786200-40792000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr21:40786400-40786600	Enhancers	Fetal Heart	heart
47	chr21:40786400-40788000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40786400-40788000	Weak transcription	Fetal Stomach	stomach
49	chr21:40786400-40792400	Weak transcription	Thymus	Thymus

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