Variant report

Variant	rs2782544
Chromosome Location	chr1:61784293-61784294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:61777609..61779531-chr1:61779675..61784488,4	K562	blood:
2	chr1:59245570..59248484-chr1:61782798..61784305,2	K562	blood:
3	chr1:61783085..61786028-chr1:61788145..61790007,2	MCF-7	breast:
4	chr1:61733972..61736610-chr1:61780635..61784681,3	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11207730	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12022282	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12036069	0.87[EUR][1000 genomes]
rs12036079	0.87[EUR][1000 genomes]
rs2782541	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2806436	0.93[CEU][hapmap]
rs2806438	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2806440	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2806441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61770523	0.89[EUR][1000 genomes]
rs6587915	0.94[EUR][1000 genomes]
rs766489	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS 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	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2782544	NPEPL1	trans	cerebellum	SCAN
rs2782544	MYSM1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61744600-61798600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:61768000-61784400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:61768800-61784400	Weak transcription	A549	lung
4	chr1:61776000-61784600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:61778400-61792800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:61779000-61784600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:61779200-61785200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:61780000-61784400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:61780000-61784600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:61782200-61788600	Weak transcription	Fetal Brain Female	brain
11	chr1:61782400-61784600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:61782400-61785400	Weak transcription	Spleen	Spleen
13	chr1:61783600-61784600	Flanking Active TSS	NHEK	skin
14	chr1:61783600-61784800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:61783600-61785000	Enhancers	HUVEC	blood vessel
16	chr1:61783800-61784400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:61783800-61784600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:61783800-61784800	Enhancers	Fetal Kidney	kidney
19	chr1:61783800-61784800	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr1:61783800-61785000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:61783800-61785000	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:61783800-61785000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:61783800-61785000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:61783800-61785000	Enhancers	HMEC	breast
25	chr1:61783800-61785600	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:61783800-61786000	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:61784000-61784400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:61784000-61784400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:61784000-61784400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:61784000-61784400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:61784000-61784400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:61784000-61784400	Active TSS	Aorta	Aorta
33	chr1:61784000-61784400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:61784000-61784400	Active TSS	NHLF	lung
35	chr1:61784000-61784600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:61784000-61784600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:61784000-61784600	Enhancers	Right Ventricle	heart
38	chr1:61784000-61784600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:61784000-61784600	Bivalent Enhancer	NH-A	brain
40	chr1:61784000-61784800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:61784000-61784800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:61784000-61784800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:61784000-61784800	Enhancers	Esophagus	oesophagus
44	chr1:61784000-61784800	Flanking Active TSS	Fetal Heart	heart
45	chr1:61784000-61784800	Flanking Active TSS	Fetal Lung	lung
46	chr1:61784000-61784800	Enhancers	Gastric	stomach
47	chr1:61784000-61784800	Enhancers	Left Ventricle	heart
48	chr1:61784000-61784800	Enhancers	Pancreas	Pancrea
49	chr1:61784000-61784800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr1:61784000-61784800	Enhancers	HSMM	muscle

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