Variant report

Variant	rs5744122
Chromosome Location	chr1:223312545-223312546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223311533..223314395-chr1:223314636..223318058,5	K562	blood:
2	chr1:223295440..223297086-chr1:223310909..223313590,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187554	Chromatin interaction
ENSG00000236846	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11485988	1.00[AMR][1000 genomes]
rs11488551	1.00[AMR][1000 genomes]
rs1417744	1.00[MEX][hapmap]
rs1640803	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1935305	1.00[YRI][hapmap]
rs2253649	1.00[MEX][hapmap]
rs28520264	1.00[EUR][1000 genomes]
rs34071437	1.00[AMR][1000 genomes]
rs35169648	1.00[AMR][1000 genomes]
rs35227692	1.00[AMR][1000 genomes]
rs35412940	1.00[AMR][1000 genomes]
rs35551279	1.00[AMR][1000 genomes]
rs35644560	1.00[AMR][1000 genomes]
rs35778136	1.00[AMR][1000 genomes]
rs3768284	1.00[MEX][hapmap]
rs5744167	1.00[MEX][hapmap]
rs5744171	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs5744175	1.00[EUR][1000 genomes]
rs5744177	1.00[EUR][1000 genomes]
rs712862	1.00[CEU][hapmap]
rs73118152	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73118170	1.00[AMR][1000 genomes]
rs73118175	1.00[AMR][1000 genomes]
rs73118176	1.00[AMR][1000 genomes]
rs73118177	1.00[AMR][1000 genomes]
rs73118181	1.00[AMR][1000 genomes]
rs73118186	1.00[AMR][1000 genomes]
rs73118187	1.00[AMR][1000 genomes]
rs73118190	1.00[AMR][1000 genomes]
rs73118193	1.00[AMR][1000 genomes]
rs73118194	1.00[AMR][1000 genomes]
rs73118198	1.00[AMR][1000 genomes]
rs73118201	1.00[AMR][1000 genomes]
rs73118202	1.00[AMR][1000 genomes]
rs73120203	1.00[AMR][1000 genomes]
rs73120204	1.00[AMR][1000 genomes]
rs73120206	1.00[AMR][1000 genomes]
rs73120207	1.00[AMR][1000 genomes]
rs73120214	1.00[AMR][1000 genomes]
rs73120219	1.00[AMR][1000 genomes]
rs73120222	1.00[AMR][1000 genomes]
rs73120224	1.00[AMR][1000 genomes]
rs73120229	1.00[AMR][1000 genomes]
rs73120232	1.00[AMR][1000 genomes]
rs73120234	1.00[AMR][1000 genomes]
rs73120236	1.00[AMR][1000 genomes]
rs73120250	1.00[AMR][1000 genomes]
rs73120257	1.00[AMR][1000 genomes]
rs73120261	1.00[AMR][1000 genomes]
rs73120265	1.00[AMR][1000 genomes]
rs73120297	1.00[AMR][1000 genomes]
rs825126	1.00[MEX][hapmap]
rs851140	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs851147	1.00[CEU][hapmap]
rs851148	1.00[CEU][hapmap]
rs851151	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs851152	1.00[CEU][hapmap]
rs851153	1.00[CEU][hapmap]
rs851195	1.00[MEX][hapmap]
rs851197	1.00[MEX][hapmap]
rs851200	1.00[MEX][hapmap]
rs860372	1.00[CEU][hapmap]

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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
3	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
4	chr1:223307800-223312600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:223308800-223314000	Weak transcription	Gastric	stomach
7	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
8	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
11	chr1:223309000-223314200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
13	chr1:223309400-223316000	Weak transcription	NHLF	lung
14	chr1:223309600-223314600	Weak transcription	Ovary	ovary
15	chr1:223309600-223314600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:223309800-223313000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:223309800-223313600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:223309800-223314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:223310600-223314000	Weak transcription	Esophagus	oesophagus
22	chr1:223310600-223314000	Weak transcription	Psoas Muscle	Psoas
23	chr1:223310600-223314200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:223310600-223315400	Weak transcription	Lung	lung
25	chr1:223311000-223314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:223311200-223314000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:223311200-223314000	Weak transcription	NHDF-Ad	bronchial
28	chr1:223311200-223314200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:223311200-223314200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:223311200-223314400	Weak transcription	HMEC	breast
31	chr1:223311200-223314400	Weak transcription	NHEK	skin
32	chr1:223311200-223314600	Weak transcription	Stomach Mucosa	stomach
33	chr1:223311200-223315800	Weak transcription	Hela-S3	cervix
34	chr1:223311200-223316000	Weak transcription	Liver	Liver
35	chr1:223311400-223314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:223311400-223314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:223311400-223316000	Weak transcription	Fetal Intestine Large	intestine
38	chr1:223311600-223312600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr1:223311600-223313000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:223311600-223313800	Weak transcription	Placenta	Placenta
41	chr1:223311600-223313800	Weak transcription	Fetal Thymus	thymus
42	chr1:223311600-223314000	Weak transcription	Adipose Nuclei	Adipose
43	chr1:223311600-223314000	Weak transcription	Brain Anterior Caudate	brain
44	chr1:223311600-223314000	Weak transcription	Fetal Lung	lung
45	chr1:223311600-223314200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:223311600-223315600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:223311600-223316000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:223312000-223314000	Weak transcription	Fetal Stomach	stomach
50	chr1:223312200-223312600	Weak transcription	Primary B cells from cord blood	blood

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