Variant report

Variant	rs2236894
Chromosome Location	chr1:209812738-209812739
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209809942..209814194-chr1:209821440..209824587,3	K562	blood:
2	chr1:209806336..209810218-chr1:209810896..209813908,3	K562	blood:
3	chr1:209810766..209813605-chr1:209813693..209816208,2	K562	blood:
4	chr1:209810488..209814194-chr1:209821440..209824229,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf74-7	chr1:209812326-209812742	expReg_chr1_20186_-

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2072941	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2236895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2282733	0.96[ASN][1000 genomes]
rs4844482	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7519594	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2236894	LAMB3	cis	parietal	SCAN
rs2236894	CDK18	cis	cerebellum	SCAN
rs2236894	CTSE	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209787400-209816200	Strong transcription	NHEK	skin
2	chr1:209799800-209814600	Strong transcription	Fetal Intestine Small	intestine
3	chr1:209800000-209813200	Strong transcription	Fetal Intestine Large	intestine
4	chr1:209801200-209814800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:209801400-209812800	Weak transcription	Pancreas	Pancrea
6	chr1:209801400-209814800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:209801600-209814600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:209801600-209818000	Weak transcription	Spleen	Spleen
9	chr1:209801600-209819800	Weak transcription	Lung	lung
10	chr1:209803600-209813200	Strong transcription	Hela-S3	cervix
11	chr1:209804400-209816600	Weak transcription	Small Intestine	intestine
12	chr1:209805200-209814600	Weak transcription	Adipose Nuclei	Adipose
13	chr1:209805400-209814600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:209805400-209814600	Weak transcription	Right Ventricle	heart
15	chr1:209805400-209816200	Weak transcription	Esophagus	oesophagus
16	chr1:209806200-209813200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:209808000-209814400	Weak transcription	Fetal Stomach	stomach
18	chr1:209808000-209816200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:209808400-209815800	Weak transcription	Colonic Mucosa	Colon
20	chr1:209808600-209814600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:209808800-209812800	Weak transcription	Fetal Heart	heart
22	chr1:209809400-209814800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:209809800-209813600	Genic enhancers	HMEC	breast
24	chr1:209810200-209812800	Weak transcription	Left Ventricle	heart
25	chr1:209810200-209814600	Weak transcription	Right Atrium	heart
26	chr1:209811000-209814600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:209811400-209812800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:209811400-209814800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:209811400-209814800	Weak transcription	Psoas Muscle	Psoas
30	chr1:209811600-209813600	Strong transcription	Stomach Mucosa	stomach
31	chr1:209811800-209812800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:209811800-209814800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:209811800-209814800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:209812000-209813000	Weak transcription	Gastric	stomach
35	chr1:209812000-209813200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:209812000-209814600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:209812200-209814800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:209812600-209813200	Enhancers	Placenta	Placenta
39	chr1:209812600-209813600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:209812600-209813800	Enhancers	Fetal Muscle Leg	muscle

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