Variant report

Variant	rs6457980
Chromosome Location	chr6:37050636-37050637
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37028754..37030470-chr6:37049218..37051479,2	K562	blood:
2	chr6:37024864..37027395-chr6:37049867..37052313,2	K562	blood:
3	chr6:37035293..37037113-chr6:37048095..37050950,2	K562	blood:
4	chr6:37040241..37044221-chr6:37049851..37052927,3	K562	blood:
5	chr6:37027099..37030994-chr6:37049896..37053173,4	MCF-7	breast:
6	chr6:37050127..37052554-chr6:37069318..37071182,2	MCF-7	breast:
7	chr6:37045453..37048349-chr6:37049676..37051329,3	K562	blood:
8	chr6:37050093..37053026-chr6:37139819..37142668,2	K562	blood:
9	chr6:37047930..37050667-chr6:37174268..37176319,2	K562	blood:
10	chr6:37045369..37048087-chr6:37049023..37051325,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10223714	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216069	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1224487	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1224488	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2094575	0.88[ASN][1000 genomes]
rs2149336	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4317401	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs4711483	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714035	0.85[EUR][1000 genomes]
rs6457974	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6457976	0.86[ASN][1000 genomes]
rs6457978	0.91[ASN][1000 genomes]
rs6457979	0.87[ASN][1000 genomes]
rs6917684	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6924660	0.88[ASN][1000 genomes]
rs6939869	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7748291	0.90[ASN][1000 genomes]
rs7750403	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs7750614	0.88[ASN][1000 genomes]
rs7750717	0.88[ASN][1000 genomes]
rs7751821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770544	0.88[ASN][1000 genomes]
rs7774073	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs831487	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs831489	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs831491	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs831497	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs831500	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs831502	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs913499	0.85[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs913500	0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs9296207	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9296208	0.88[ASN][1000 genomes]
rs9366927	0.89[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380637	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9380638	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394401	0.90[ASN][1000 genomes]
rs9394402	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394403	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462258	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470469	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6457980	FGD2	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37040000-37051200	Weak transcription	A549	lung
2	chr6:37045800-37051000	Weak transcription	Colonic Mucosa	Colon
3	chr6:37045800-37051000	Weak transcription	Left Ventricle	heart
4	chr6:37045800-37051000	Weak transcription	Lung	lung
5	chr6:37045800-37051000	Weak transcription	Right Atrium	heart
6	chr6:37045800-37051400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:37045800-37060800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:37046000-37051000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:37046000-37051000	Weak transcription	Esophagus	oesophagus
10	chr6:37046000-37051000	Weak transcription	Right Ventricle	heart
11	chr6:37046000-37051200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:37046200-37051000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:37046200-37051000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:37046200-37051000	Weak transcription	NHEK	skin
15	chr6:37046400-37051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:37046400-37051000	Weak transcription	Fetal Lung	lung
17	chr6:37046600-37051000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:37046800-37050800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:37046800-37051200	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:37047000-37051000	Weak transcription	Fetal Stomach	stomach
21	chr6:37047000-37051000	Weak transcription	Osteobl	bone
22	chr6:37047000-37051200	Weak transcription	NHLF	lung
23	chr6:37047200-37051200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:37047600-37050800	Enhancers	HepG2	liver
25	chr6:37047600-37051000	Weak transcription	NHDF-Ad	bronchial
26	chr6:37048800-37052600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:37049000-37051000	Enhancers	K562	blood
28	chr6:37049200-37051000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:37049600-37052200	Enhancers	Adipose Nuclei	Adipose
30	chr6:37049600-37052800	Enhancers	Fetal Intestine Large	intestine
31	chr6:37049600-37053200	Enhancers	Fetal Intestine Small	intestine
32	chr6:37049800-37051000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:37049800-37052400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:37050000-37050800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr6:37050400-37050800	Weak transcription	Spleen	Spleen
36	chr6:37050400-37052200	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:37050400-37052400	Enhancers	Placenta	Placenta
38	chr6:37050400-37052600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr6:37050400-37053200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:37050600-37051200	Flanking Active TSS	Liver	Liver
41	chr6:37050600-37051800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:37050600-37051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:37050600-37051800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr6:37050600-37051800	Enhancers	HMEC	breast
45	chr6:37050600-37052000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:37050600-37052600	Enhancers	Primary hematopoietic stem cells	blood
47	chr6:37050600-37052800	Enhancers	Ovary	ovary

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