Variant report

Variant	rs776602
Chromosome Location	chr4:48611929-48611930
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr4:48611854-48612159	HepG2	liver:	n/a	chr4:48612005-48612023
2	MAFK	chr4:48611881-48612149	HepG2	liver:	n/a	chr4:48612006-48612021
3	MAFK	chr4:48611907-48612123	HepG2	liver:	n/a	chr4:48612006-48612021

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48610440..48612652-chr4:48613974..48616087,2	MCF-7	breast:

Variant related genes	Relation type
FRYL	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12645501	0.85[YRI][hapmap]
rs13141523	0.85[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs1507865	0.85[YRI][hapmap]
rs16861510	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1702797	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17656094	0.85[YRI][hapmap]
rs2102397	0.92[YRI][hapmap]
rs2176460	0.85[YRI][hapmap]
rs2354938	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4404518	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4536901	0.85[YRI][hapmap]
rs4695391	0.85[YRI][hapmap]
rs62309671	0.90[ASN][1000 genomes]
rs62309745	0.80[AMR][1000 genomes]
rs6811148	0.85[YRI][hapmap]
rs6834782	0.87[ASN][1000 genomes]
rs7657698	0.85[YRI][hapmap]
rs7697522	0.85[YRI][hapmap]
rs776584	0.85[YRI][hapmap]
rs776591	0.85[YRI][hapmap]
rs776604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796555	0.85[YRI][hapmap]
rs937888	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv966557	chr4:48577320-48618907	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs776602	GABRG1	cis	cerebellum	SCAN
rs776602	TXK	cis	parietal	SCAN
rs776602	OCIAD2	cis	cerebellum	SCAN
rs776602	TEC	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
2	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
7	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
8	chr4:48579600-48615800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:48588800-48619600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:48590200-48614000	Weak transcription	Fetal Kidney	kidney
12	chr4:48590600-48627600	Weak transcription	Fetal Brain Female	brain
13	chr4:48590800-48619600	Weak transcription	Fetal Stomach	stomach
14	chr4:48590800-48619600	Weak transcription	Lung	lung
15	chr4:48591000-48618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:48591000-48619400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:48591200-48626600	Weak transcription	Ovary	ovary
18	chr4:48591400-48619600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:48591800-48619000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:48592200-48623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:48592400-48620800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:48592600-48619600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:48593400-48614000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:48594000-48619600	Weak transcription	Aorta	Aorta
25	chr4:48594000-48622600	Weak transcription	Psoas Muscle	Psoas
26	chr4:48594000-48637400	Weak transcription	Spleen	Spleen
27	chr4:48596800-48619000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:48597000-48619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:48597000-48620800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:48597200-48613800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:48597200-48614000	Weak transcription	Brain Anterior Caudate	brain
32	chr4:48597400-48619600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:48597600-48618600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:48597800-48614400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:48598000-48615400	Weak transcription	Fetal Thymus	thymus
37	chr4:48598000-48623000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:48598200-48634800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:48598600-48618800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:48598600-48619600	Weak transcription	GM12878-XiMat	blood
41	chr4:48598800-48619200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:48599400-48620400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:48600600-48616000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr4:48601000-48620800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:48601800-48614000	Weak transcription	Adipose Nuclei	Adipose
46	chr4:48601800-48619800	Weak transcription	Placenta	Placenta
47	chr4:48602200-48619400	Weak transcription	Thymus	Thymus
48	chr4:48602400-48613800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:48602600-48613800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:48605000-48617800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links