Variant report

Variant	rs5744110
Chromosome Location	chr1:223315076-223315077
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223305699..223307476-chr1:223314416..223316383,2	K562	blood:
2	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:
3	chr1:223314112..223315763-chr1:223428668..223430244,2	MCF-7	breast:
4	chr1:223309835..223312758-chr1:223314072..223315827,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUSD4-2	chr1:223314990-223315105	NONHSAT009730
2	lnc-SUSD4-2	chr1:223314724-223315105	NONHSAT009731

No data

Variant related genes	Relation type
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1624408	1.00[EUR][1000 genomes]
rs1640869	1.00[EUR][1000 genomes]
rs28373518	1.00[EUR][1000 genomes]
rs28445941	1.00[EUR][1000 genomes]
rs28488039	1.00[EUR][1000 genomes]
rs28782805	1.00[EUR][1000 genomes]
rs35801972	1.00[EUR][1000 genomes]
rs6658085	1.00[EUR][1000 genomes]
rs6693240	1.00[EUR][1000 genomes]
rs725972	1.00[EUR][1000 genomes]
rs74145707	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
2	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
3	chr1:223309400-223316000	Weak transcription	NHLF	lung
4	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:223310600-223315400	Weak transcription	Lung	lung
7	chr1:223311200-223315800	Weak transcription	Hela-S3	cervix
8	chr1:223311200-223316000	Weak transcription	Liver	Liver
9	chr1:223311400-223316000	Weak transcription	Fetal Intestine Large	intestine
10	chr1:223311600-223315600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:223311600-223316000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:223313400-223315600	Enhancers	Fetal Muscle Leg	muscle
14	chr1:223313600-223315800	Enhancers	Fetal Muscle Trunk	muscle
15	chr1:223313800-223315800	Enhancers	Placenta	Placenta
16	chr1:223314000-223315400	Enhancers	Primary B cells from cord blood	blood
17	chr1:223314000-223315600	Enhancers	Gastric	stomach
18	chr1:223314000-223315800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:223314000-223315800	Enhancers	Esophagus	oesophagus
20	chr1:223314000-223315800	Enhancers	Pancreas	Pancrea
21	chr1:223314000-223316000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:223314200-223315400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:223314200-223315600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:223314200-223315600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:223314200-223316000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:223314200-223316000	Enhancers	Right Ventricle	heart
27	chr1:223314200-223316000	Enhancers	HSMMtube	muscle
28	chr1:223314400-223315800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:223314400-223316000	Weak transcription	Psoas Muscle	Psoas
30	chr1:223314600-223315400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:223314600-223315600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:223314600-223315600	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:223314600-223315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:223314800-223315200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:223314800-223315200	Enhancers	Adipose Nuclei	Adipose
36	chr1:223314800-223315200	Weak transcription	Ovary	ovary
37	chr1:223314800-223315200	Weak transcription	Stomach Mucosa	stomach
38	chr1:223314800-223315200	Weak transcription	Spleen	Spleen
39	chr1:223314800-223315400	Enhancers	Brain Anterior Caudate	brain
40	chr1:223314800-223315600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:223314800-223315600	Weak transcription	Brain Substantia Nigra	brain
42	chr1:223314800-223315600	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:223314800-223315600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:223314800-223315800	Weak transcription	Fetal Heart	heart
45	chr1:223314800-223315800	Weak transcription	Fetal Lung	lung
46	chr1:223314800-223315800	Weak transcription	Left Ventricle	heart
47	chr1:223314800-223315800	Weak transcription	HMEC	breast
48	chr1:223314800-223316000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:223314800-223316000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:223314800-223316000	Weak transcription	Placenta Amnion	Placenta Amnion

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