Variant report

Variant	rs2428161
Chromosome Location	chr7:104592567-104592568
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:104591428..104594031-chr7:104654268..104656981,2	MCF-7	breast:
2	chr7:104591318..104592948-chr7:104653060..104655633,2	MCF-7	breast:
3	chr7:104591329..104593966-chr7:104601076..104603723,3	K562	blood:
4	chr7:104592416..104594450-chr7:104601446..104605080,3	K562	blood:
5	chr7:104592455..104594379-chr7:104649567..104651411,2	K562	blood:
6	chr7:104591217..104594186-chr7:104651548..104654499,3	K562	blood:
7	chr7:104581950..104584556-chr7:104591161..104593888,2	K562	blood:
8	chr7:104590688..104592595-chr7:104595872..104597993,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239569	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000005483	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10953459	0.80[ASN][1000 genomes]
rs11978074	0.81[ASN][1000 genomes]
rs13237211	0.99[ASN][1000 genomes]
rs17777642	0.85[ASN][1000 genomes]
rs2252074	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2428162	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2470942	0.82[CEU][hapmap]
rs2470943	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs2470945	0.82[CEU][hapmap]
rs2470951	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60137855	0.80[ASN][1000 genomes]
rs6466030	0.97[ASN][1000 genomes]
rs6466031	0.83[ASN][1000 genomes]
rs6466033	0.85[ASN][1000 genomes]
rs6466034	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs740068	0.86[JPT][hapmap]
rs7795893	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7807853	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs886145	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[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	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2428161	RINT1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104584600-104619000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:104586800-104596800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:104587000-104597000	Weak transcription	Fetal Stomach	stomach
4	chr7:104587000-104597600	Weak transcription	Right Atrium	heart
5	chr7:104587200-104595600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:104587200-104596800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:104587200-104597000	Weak transcription	Fetal Thymus	thymus
8	chr7:104587200-104599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:104587200-104600800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:104587200-104623600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:104587400-104595800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:104587400-104597000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr7:104588000-104597000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:104588800-104596800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:104589200-104595600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:104589200-104595800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:104589400-104596200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:104590600-104594600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:104590800-104595600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr7:104591000-104592600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr7:104591000-104592600	Enhancers	Adipose Nuclei	Adipose
22	chr7:104591000-104594800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:104591200-104592600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:104591200-104593000	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr7:104591200-104593000	Enhancers	NHDF-Ad	bronchial
26	chr7:104591200-104595800	Weak transcription	Primary B cells from cord blood	blood
27	chr7:104591400-104596800	Weak transcription	Small Intestine	intestine
28	chr7:104591600-104593000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr7:104591600-104604600	Weak transcription	Fetal Kidney	kidney
30	chr7:104591800-104592600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:104592000-104592600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr7:104592000-104592800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:104592200-104592600	Enhancers	Osteobl	bone
34	chr7:104592200-104593800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:104592200-104595600	Weak transcription	Stomach Mucosa	stomach
36	chr7:104592200-104595800	Weak transcription	NHLF	lung
37	chr7:104592400-104592800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:104592400-104597200	Weak transcription	NH-A	brain

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