Variant report

Variant	rs6800954
Chromosome Location	chr3:45964959-45964960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45943266..45944977-chr3:45963147..45965893,2	MCF-7	breast:
2	chr3:45952412..45954426-chr3:45964464..45966839,2	K562	blood:

Variant related genes	Relation type
ENSG00000201635	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1072755	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs12054287	0.88[CEU][hapmap]
rs13066048	0.80[CHB][hapmap]
rs1552489	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs17078449	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17078454	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054866	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs2234351	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2234358	0.80[CHB][hapmap];0.84[CHD][hapmap]
rs2248228	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs35537559	0.83[EUR][1000 genomes]
rs3733103	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs3774638	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774639	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs3774640	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796373	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap]
rs3796376	0.89[CEU][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs3821883	0.83[EUR][1000 genomes]
rs4535265	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs4682799	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs4682800	0.82[CHB][hapmap]
rs4683148	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs4683153	0.94[ASN][1000 genomes]
rs57204020	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59226168	0.82[EUR][1000 genomes]
rs59767267	0.82[EUR][1000 genomes]
rs60237998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60779624	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62242787	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62242788	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62242796	0.83[EUR][1000 genomes]
rs62245106	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62245108	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6778225	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778324	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781121	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs6781668	0.83[EUR][1000 genomes]
rs7129	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs7623476	0.85[CEU][hapmap]
rs7631809	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643426	0.83[CEU][hapmap]
rs936938	0.85[CHB][hapmap]
rs936939	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831315	0.82[CHB][hapmap]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6800954	FYCO1	cis	brain	BrainEAC

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45957600-45965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:45957800-45969000	Weak transcription	K562	blood
3	chr3:45957800-45971200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:45958000-45965000	Weak transcription	Osteobl	bone
5	chr3:45958000-45965200	Weak transcription	HSMM	muscle
6	chr3:45958000-45969000	Weak transcription	NH-A	brain
7	chr3:45958000-45980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:45958400-45966200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr3:45958400-45974200	Strong transcription	Fetal Stomach	stomach
10	chr3:45958600-45968800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:45958600-45970000	Weak transcription	Small Intestine	intestine
12	chr3:45958800-45980000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:45958800-45980200	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
15	chr3:45959000-45966000	Genic enhancers	Fetal Thymus	thymus
16	chr3:45959000-45973600	Weak transcription	Fetal Kidney	kidney
17	chr3:45959200-45979800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:45959200-45980400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:45959400-45965000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:45959400-45965200	Weak transcription	HMEC	breast
21	chr3:45959400-45965800	Genic enhancers	Thymus	Thymus
22	chr3:45959400-45965800	Genic enhancers	Dnd41	blood
23	chr3:45959400-45966000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr3:45959400-45971800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:45959400-45973400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:45959600-45965600	Strong transcription	Brain Cingulate Gyrus	brain
28	chr3:45959600-45973200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:45959800-45965600	Weak transcription	Hela-S3	cervix
30	chr3:45959800-45974600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:45959800-45979800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:45959800-45979800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:45959800-45980400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:45960000-45965800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:45960000-45965800	Strong transcription	Adipose Nuclei	Adipose
36	chr3:45960000-45966000	Strong transcription	Liver	Liver
37	chr3:45960000-45966200	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:45960000-45967800	Strong transcription	Placenta	Placenta
39	chr3:45960000-45979400	Strong transcription	Fetal Intestine Large	intestine
40	chr3:45960000-45980400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:45960200-45965200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:45960200-45965800	Strong transcription	Esophagus	oesophagus
43	chr3:45960200-45965800	Strong transcription	Spleen	Spleen
44	chr3:45960200-45966000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:45960200-45966000	Strong transcription	Lung	lung
46	chr3:45960200-45966000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:45960200-45974200	Strong transcription	Fetal Intestine Small	intestine
48	chr3:45960400-45965800	Strong transcription	Primary B cells from cord blood	blood
49	chr3:45960400-45965800	Strong transcription	Pancreas	Pancrea
50	chr3:45960400-45966000	Strong transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links