Variant report

Variant	rs9878005
Chromosome Location	chr3:178899867-178899868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178899642..178902077-chr3:178904169..178907313,3	K562	blood:
2	chr3:178898456..178900555-chr3:179010797..179013245,2	K562	blood:
3	chr3:178898160..178900976-chr3:178901666..178903620,2	K562	blood:
4	chr3:178899086..178902051-chr3:178909040..178911935,2	K562	blood:
5	chr3:178899086..178902333-chr3:178909040..178911935,3	K562	blood:
6	chr3:178864222..178867700-chr3:178899476..178901902,3	K562	blood:

Variant related genes	Relation type
ENSG00000121879	Chromatin interaction
ENSG00000229102	Chromatin interaction

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

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

rs_ID	r²[population]
rs10936993	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12486399	0.98[EUR][1000 genomes]
rs12497857	0.94[EUR][1000 genomes]
rs13320527	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1517585	1.00[EUR][1000 genomes]
rs2865084	0.98[EUR][1000 genomes]
rs28697961	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45455192	0.96[EUR][1000 genomes]
rs4854906	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4854940	1.00[EUR][1000 genomes]
rs4854955	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4854976	0.98[EUR][1000 genomes]
rs4855094	1.00[EUR][1000 genomes]
rs60713157	0.83[EUR][1000 genomes]
rs61404287	0.94[EUR][1000 genomes]
rs61796464	1.00[EUR][1000 genomes]
rs61796465	0.98[EUR][1000 genomes]
rs61796466	1.00[EUR][1000 genomes]
rs61796467	1.00[EUR][1000 genomes]
rs61798205	0.83[EUR][1000 genomes]
rs61798206	0.83[EUR][1000 genomes]
rs61798207	0.83[EUR][1000 genomes]
rs61798211	0.94[EUR][1000 genomes]
rs61798213	0.94[EUR][1000 genomes]
rs6443623	0.98[EUR][1000 genomes]
rs6791215	0.94[EUR][1000 genomes]
rs6804195	0.83[EUR][1000 genomes]
rs73051979	1.00[EUR][1000 genomes]
rs73054091	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7374077	0.90[EUR][1000 genomes]
rs7615259	0.98[EUR][1000 genomes]
rs950486	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9758036	0.83[EUR][1000 genomes]
rs9812252	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9819654	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823044	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9833206	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9860843	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9872959	0.94[AMR][1000 genomes];0.96[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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv963506	chr3:178897583-178904531	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv524471	chr3:178897674-178903264	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178867800-178900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:178883800-178905800	Weak transcription	Fetal Kidney	kidney
3	chr3:178887200-178912000	Weak transcription	Thymus	Thymus
4	chr3:178893000-178900200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:178893800-178900800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:178894200-178905800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:178894400-178903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:178895600-178904400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:178896200-178900000	Enhancers	Primary T cells from cord blood	blood
10	chr3:178896200-178900600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:178896200-178903600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:178896400-178900000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:178896400-178902800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr3:178896400-178905000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:178896600-178900000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:178896600-178900600	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr3:178896600-178900800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:178896600-178902200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:178896600-178904200	Enhancers	Colon Smooth Muscle	Colon
20	chr3:178896800-178900200	Weak transcription	Left Ventricle	heart
21	chr3:178896800-178900200	Weak transcription	Right Atrium	heart
22	chr3:178896800-178902000	Weak transcription	Gastric	stomach
23	chr3:178896800-178912200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:178896800-178912400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:178897000-178900000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:178897000-178900200	Weak transcription	Ovary	ovary
27	chr3:178897000-178900800	Enhancers	HSMM	muscle
28	chr3:178897000-178901800	Weak transcription	Psoas Muscle	Psoas
29	chr3:178897000-178902000	Weak transcription	Aorta	Aorta
30	chr3:178897400-178900800	Enhancers	Osteobl	bone
31	chr3:178897600-178900600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:178897600-178900600	Enhancers	Brain Hippocampus Middle	brain
33	chr3:178897600-178900800	Enhancers	Brain Anterior Caudate	brain
34	chr3:178897600-178901000	Enhancers	Brain Substantia Nigra	brain
35	chr3:178897600-178901000	Enhancers	NHDF-Ad	bronchial
36	chr3:178897600-178901000	Enhancers	NHLF	lung
37	chr3:178897600-178904600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr3:178897800-178900000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:178897800-178900000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:178897800-178900200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr3:178897800-178900400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr3:178897800-178900600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:178897800-178901000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:178897800-178906800	Weak transcription	Fetal Stomach	stomach
45	chr3:178897800-178919400	Weak transcription	Fetal Intestine Small	intestine
46	chr3:178898000-178900400	Enhancers	NH-A	brain
47	chr3:178898000-178900600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr3:178898000-178900800	Enhancers	Rectal Smooth Muscle	rectum
49	chr3:178898000-178901000	Enhancers	Brain Germinal Matrix	brain
50	chr3:178898000-178901200	Enhancers	Liver	Liver

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