Variant report

Variant	rs2024789
Chromosome Location	chr1:61817001-61817002
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:61815681..61817818-chr1:61903758..61906179,2	K562	blood:
2	chr1:61813440..61817104-chr1:61817540..61820998,4	K562	blood:

Variant related genes	Relation type
ENSG00000162599	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1041674	0.86[JPT][hapmap]
rs1125777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207787	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2364466	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364475	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2782540	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2806435	0.86[JPT][hapmap]
rs2806442	0.82[JPT][hapmap]
rs41350144	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs41453448	1.00[YRI][hapmap]
rs6691768	0.86[JPT][hapmap]
rs7521242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7553528	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7556462	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9436636	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv1014023	chr1:61788310-61859074	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv534981	chr1:61788310-61859074	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2024789	PRSS21	trans	lymphoblastoid	seeQTL
rs2024789	RPS25	trans	parietal	SCAN
rs2024789	MYSM1	cis	cerebellum	SCAN
rs2024789	MYSM1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61801000-61818600	Weak transcription	K562	blood
2	chr1:61801200-61824600	Weak transcription	Gastric	stomach
3	chr1:61804400-61818200	Weak transcription	Fetal Brain Male	brain
4	chr1:61804400-61818400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:61804400-61818400	Weak transcription	Hela-S3	cervix
6	chr1:61804400-61851400	Weak transcription	Small Intestine	intestine
7	chr1:61804400-61854600	Weak transcription	Placenta	Placenta
8	chr1:61804600-61818200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:61804800-61822800	Weak transcription	Fetal Stomach	stomach
10	chr1:61805000-61818200	Weak transcription	A549	lung
11	chr1:61805000-61818400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:61805600-61817600	Weak transcription	HUVEC	blood vessel
13	chr1:61805800-61818000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:61805800-61818200	Weak transcription	Esophagus	oesophagus
15	chr1:61805800-61818600	Weak transcription	Lung	lung
16	chr1:61805800-61848800	Weak transcription	Pancreas	Pancrea
17	chr1:61809400-61818400	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:61810000-61818800	Weak transcription	Fetal Brain Female	brain
19	chr1:61810000-61822600	Weak transcription	Fetal Kidney	kidney
20	chr1:61810200-61824600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:61810200-61827600	Weak transcription	Brain Germinal Matrix	brain
22	chr1:61810400-61818200	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:61810400-61818600	Weak transcription	Aorta	Aorta
24	chr1:61810400-61824200	Weak transcription	Fetal Intestine Small	intestine
25	chr1:61810400-61828000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:61810600-61818200	Weak transcription	Fetal Heart	heart
27	chr1:61810600-61818200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:61810600-61824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:61810600-61828000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:61810600-61831600	Weak transcription	Stomach Mucosa	stomach
31	chr1:61810800-61824400	Weak transcription	Brain Anterior Caudate	brain
32	chr1:61810800-61827800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:61811000-61822400	Weak transcription	Colonic Mucosa	Colon
34	chr1:61811400-61818400	Weak transcription	Ovary	ovary
35	chr1:61811600-61818200	Weak transcription	Left Ventricle	heart
36	chr1:61812400-61819000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:61813000-61818000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:61813800-61818400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:61813800-61829800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:61814000-61818200	Weak transcription	Right Atrium	heart
41	chr1:61814000-61818400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:61814000-61848800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:61814200-61818400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:61814200-61823600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:61814600-61817800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:61814600-61818200	Weak transcription	Adipose Nuclei	Adipose
47	chr1:61814600-61818200	Weak transcription	Fetal Intestine Large	intestine
48	chr1:61814600-61818200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:61814600-61818400	Weak transcription	Fetal Lung	lung
50	chr1:61814600-61841200	Weak transcription	Psoas Muscle	Psoas

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