Variant report

Variant	rs3790507
Chromosome Location	chr1:151513247-151513248
allele	A/G
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:37)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
2	chr1:85039501..85040254-chr1:151512684..151513325,2	Hela-S3	cervix:
3	chr1:151421812..151434588-chr1:151506621..151515599,30	MCF-7	breast:
4	chr1:28969492..28970329-chr1:151512730..151513308,2	Hela-S3	cervix:
5	chr1:151512663..151513550-chr3:12525762..12526558,2	Hela-S3	cervix:
6	chr1:151494437..151499363-chr1:151510633..151514422,7	MCF-7	breast:
7	chr1:151512783..151513434-chr9:131037787..131038660,2	Hela-S3	cervix:
8	chr1:151512820..151513601-chr20:33542888..33543850,2	Hela-S3	cervix:
9	chr1:151512695..151514361-chr1:151804056..151806637,3	MCF-7	breast:
10	chr1:151511929..151514676-chr5:16935884..16938127,2	MCF-7	breast:
11	chr1:151512640..151513443-chr3:100428519..100429048,2	Hela-S3	cervix:
12	chr1:151510867..151515069-chr1:151533037..151539348,7	MCF-7	breast:
13	chr1:151510723..151515515-chr1:151802413..151805096,5	MCF-7	breast:
14	chr1:151512781..151513515-chr17:42422456..42423040,2	Hela-S3	cervix:
15	chr1:151512668..151514795-chr1:151529335..151532212,2	K562	blood:
16	chr1:151511342..151513361-chr1:151529767..151532080,2	MCF-7	breast:
17	chr1:151511592..151513482-chr9:113016876..113019727,2	MCF-7	breast:
18	chr1:151510726..151515686-chr1:151583230..151586215,6	MCF-7	breast:
19	chr1:151512334..151513279-chr10:94608004..94608822,2	Hela-S3	cervix:
20	chr1:151512313..151514089-chr3:39423180..39426141,2	MCF-7	breast:
21	chr1:151499502..151502122-chr1:151511648..151513316,2	MCF-7	breast:
22	chr1:151370811..151373589-chr1:151512732..151514796,2	K562	blood:
23	chr1:151372028..151374418-chr1:151511841..151514665,2	MCF-7	breast:
24	chr1:151477348..151494376-chr1:151504804..151515249,50	MCF-7	breast:
25	chr1:151512315..151513514-chr15:65596770..65597736,3	Hela-S3	cervix:
26	chr1:151510509..151513919-chr1:151688057..151691918,3	MCF-7	breast:
27	chr1:151510534..151515854-chr1:151533093..151539013,11	MCF-7	breast:
28	chr1:151509848..151514263-chr1:151581077..151585541,5	MCF-7	breast:
29	chr1:151512325..151513409-chr14:96967489..96968213,3	Hela-S3	cervix:
30	chr1:151512673..151514218-chr1:151769581..151771574,2	MCF-7	breast:
31	chr1:151430095..151434593-chr1:151511133..151513913,5	K562	blood:
32	chr1:151254308..151256785-chr1:151512305..151514288,3	MCF-7	breast:
33	chr1:151429106..151432636-chr1:151510898..151514410,7	MCF-7	breast:
34	chr1:151431826..151434593-chr1:151511133..151514053,3	K562	blood:
35	chr1:151511637..151514253-chr10:74032442..74033943,2	MCF-7	breast:
36	chr1:151512582..151515033-chr8:145580545..145582400,2	MCF-7	breast:
37	chr1:151511607..151513918-chr17:57914768..57918620,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGN-1	chr1:151512992-151513385	ENSG00000232536.1

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000138190	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000229388	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000182325	Chromatin interaction
ENSG00000159409	Chromatin interaction
ENSG00000154743	Chromatin interaction
ENSG00000175854	Chromatin interaction
ENSG00000120656	Chromatin interaction
ENSG00000100983	Chromatin interaction
ENSG00000145555	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000167110	Chromatin interaction
ENSG00000136810	Chromatin interaction
ENSG00000269489	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000114354	Chromatin interaction
ENSG00000185803	Chromatin interaction
ENSG00000144659	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000030582	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000168209	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000090060	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11204848	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12217027	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12746522	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12746531	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2185838	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4132646	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970961	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970962	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6673116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6691736	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9645404	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151511800-151513600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:151511800-151513800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr1:151512000-151513800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:151512000-151514800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:151512200-151513600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:151512200-151513600	Active TSS	Fetal Brain Male	brain
7	chr1:151512200-151513800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:151512200-151513800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
9	chr1:151512200-151513800	Active TSS	Fetal Kidney	kidney
10	chr1:151512200-151513800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr1:151512200-151514000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:151512200-151514000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:151512400-151513600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:151512400-151513600	Active TSS	Ovary	ovary
15	chr1:151512400-151513800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:151512400-151514000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:151512400-151514000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:151512400-151514000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:151512400-151514200	Active TSS	Brain Cingulate Gyrus	brain
20	chr1:151512400-151515600	Active TSS	Esophagus	oesophagus
21	chr1:151512600-151513400	Active TSS	Primary T cells from cord blood	blood
22	chr1:151512600-151513400	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr1:151512600-151513400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:151512600-151513400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:151512600-151513400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr1:151512600-151513400	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr1:151512600-151513400	Active TSS	Brain Anterior Caudate	brain
28	chr1:151512600-151513400	Active TSS	Brain Hippocampus Middle	brain
29	chr1:151512600-151513400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:151512600-151513400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr1:151512600-151513400	Active TSS	Hela-S3	cervix
32	chr1:151512600-151513600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:151512600-151513600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:151512600-151513600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:151512600-151513600	Active TSS	Brain Angular Gyrus	brain
36	chr1:151512600-151513600	Active TSS	Colon Smooth Muscle	Colon
37	chr1:151512600-151513600	Active TSS	Duodenum Mucosa	Duodenum
38	chr1:151512600-151513600	Active TSS	Left Ventricle	heart
39	chr1:151512600-151513600	Active TSS	Lung	lung
40	chr1:151512600-151513600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr1:151512600-151513600	Active TSS	Small Intestine	intestine
42	chr1:151512600-151513600	Bivalent/Poised TSS	HepG2	liver
43	chr1:151512600-151513800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:151512600-151513800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:151512600-151513800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:151512600-151513800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:151512600-151513800	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr1:151512600-151513800	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:151512600-151513800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:151512600-151513800	Active TSS	Muscle Satellite Cultured Cells	--

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