Variant report

Variant	rs3850854
Chromosome Location	chr1:45126035-45126036
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	chr1:45123178..45126721-chr1:45185121..45188649,3	MCF-7	breast:
2	chr1:45123055..45126216-chr1:45128563..45131707,5	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12036630	1.00[EUR][1000 genomes]
rs1321703	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16832186	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16832188	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2281759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3444	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3738733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754421	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3768441	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3889695	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41468751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs41524944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4660285	0.94[ASN][1000 genomes]
rs4660286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660814	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4660819	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660820	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs56756630	0.90[EUR][1000 genomes]
rs59834392	0.90[EUR][1000 genomes]
rs66509359	1.00[EUR][1000 genomes]
rs72671943	0.90[EUR][1000 genomes]
rs72671944	0.90[EUR][1000 genomes]
rs72671945	0.90[EUR][1000 genomes]
rs72671948	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72671949	0.87[AMR][1000 genomes]
rs72671950	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72671962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72671966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72671967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72671971	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72671974	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671982	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671984	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671988	1.00[EUR][1000 genomes]
rs7532001	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs7539607	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45104000-45138200	Weak transcription	Fetal Brain Male	brain
2	chr1:45111200-45128000	Weak transcription	Right Atrium	heart
3	chr1:45113000-45126200	Weak transcription	Small Intestine	intestine
4	chr1:45114600-45130000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:45115200-45137800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:45115800-45138000	Weak transcription	NHDF-Ad	bronchial
7	chr1:45116000-45130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:45116600-45127600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:45117200-45127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:45117200-45130200	Weak transcription	Primary B cells from cord blood	blood
11	chr1:45117200-45137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:45117200-45138600	Weak transcription	Aorta	Aorta
13	chr1:45117400-45129200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:45117400-45130200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:45117400-45130200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:45117400-45130200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:45117400-45138000	Weak transcription	Left Ventricle	heart
18	chr1:45117600-45130200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:45117800-45128000	Weak transcription	Colonic Mucosa	Colon
20	chr1:45118200-45130200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:45118400-45127600	Weak transcription	Thymus	Thymus
22	chr1:45118400-45129400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:45118400-45130000	Weak transcription	GM12878-XiMat	blood
24	chr1:45118400-45130200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:45118600-45138600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:45119000-45128800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:45119200-45126800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:45119200-45139200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:45119800-45138000	Weak transcription	Primary T cells from cord blood	blood
30	chr1:45120200-45129200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:45120400-45130200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:45120600-45127400	Weak transcription	Placenta	Placenta
33	chr1:45120800-45126800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:45120800-45127400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:45120800-45130400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:45120800-45134200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:45121000-45126200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:45121000-45129200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:45121000-45137600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:45121000-45138600	Weak transcription	Gastric	stomach
41	chr1:45121200-45126800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:45121200-45130400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:45123400-45132200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:45124800-45126200	Enhancers	Brain Angular Gyrus	brain
45	chr1:45124800-45126400	Enhancers	Fetal Heart	heart
46	chr1:45124800-45126800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:45124800-45129200	Enhancers	Fetal Muscle Trunk	muscle
48	chr1:45125000-45126400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:45125000-45126400	Enhancers	Pancreas	Pancrea
50	chr1:45125000-45128000	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links