Variant report

Variant	rs7785049
Chromosome Location	chr7:39683560-39683561
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39678677..39680860-chr7:39681239..39684252,3	K562	blood:
2	chr7:39661973..39663935-chr7:39682940..39685459,2	MCF-7	breast:
3	chr7:39677650..39680177-chr7:39682752..39684306,2	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11769865	0.87[EUR][1000 genomes]
rs11982634	0.86[EUR][1000 genomes]
rs2107710	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2158548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158549	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189837	0.89[EUR][1000 genomes]
rs2329464	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2876862	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3823742	0.88[EUR][1000 genomes]
rs4723887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723891	0.89[EUR][1000 genomes]
rs4723892	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6462936	0.83[EUR][1000 genomes]
rs6462937	0.93[EUR][1000 genomes]
rs6952363	0.89[EUR][1000 genomes]
rs6952866	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6956681	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6961667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969070	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6969523	0.92[EUR][1000 genomes]
rs7806651	0.88[EUR][1000 genomes]
rs917077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7785049	LINC00265	cis	Thyroid	GTEx
rs7785049	LINC00265	cis	lung	GTEx
rs7785049	LINC00265	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39666200-39694400	Weak transcription	Fetal Brain Female	brain
2	chr7:39667200-39698800	Weak transcription	Fetal Kidney	kidney
3	chr7:39671800-39693800	Weak transcription	A549	lung
4	chr7:39672200-39684000	Weak transcription	NHLF	lung
5	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
6	chr7:39674000-39690200	Weak transcription	NH-A	brain
7	chr7:39674000-39690800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:39674200-39683800	Weak transcription	Spleen	Spleen
9	chr7:39674200-39690000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:39674200-39691400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:39674200-39696000	Weak transcription	Thymus	Thymus
12	chr7:39674400-39683800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:39674400-39685400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:39675200-39683800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:39675200-39708800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:39675600-39688200	Weak transcription	Fetal Stomach	stomach
17	chr7:39675600-39701400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:39675800-39691600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:39676600-39683600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:39676600-39690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:39676600-39694400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr7:39676600-39694400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:39676600-39694400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:39676800-39685200	Weak transcription	HepG2	liver
25	chr7:39677400-39694200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr7:39678000-39687800	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:39678800-39694400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr7:39679600-39695800	Weak transcription	Primary B cells from cord blood	blood
29	chr7:39679800-39683600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr7:39680000-39700800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:39680000-39701000	Weak transcription	Esophagus	oesophagus
32	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:39680400-39687400	Weak transcription	Primary T cells from cord blood	blood
34	chr7:39680600-39683800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:39680600-39684600	Weak transcription	Adipose Nuclei	Adipose
36	chr7:39680800-39683800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:39680800-39685400	Weak transcription	Right Atrium	heart
38	chr7:39680800-39685800	Weak transcription	Psoas Muscle	Psoas
39	chr7:39680800-39687000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:39680800-39689000	Weak transcription	NHDF-Ad	bronchial
41	chr7:39680800-39704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr7:39680800-39716400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr7:39681000-39686600	Enhancers	Fetal Heart	heart
44	chr7:39681200-39684000	Enhancers	HUVEC	blood vessel
45	chr7:39681800-39685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr7:39682000-39683800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr7:39682000-39683800	Weak transcription	HSMM	muscle
48	chr7:39682000-39685200	Weak transcription	Right Ventricle	heart
49	chr7:39682000-39686800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr7:39682000-39687000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links