Variant report

Variant	rs10164753
Chromosome Location	chr2:179438866-179438867
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	chr2:179434791..179437308-chr2:179438130..179440341,2	K562	blood:
2	chr2:179432790..179436322-chr2:179437819..179441282,4	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10183237	1.00[CHD][hapmap]
rs10183361	0.85[CHD][hapmap]
rs10497517	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11888217	0.83[CHD][hapmap]
rs11895382	0.83[CHD][hapmap]
rs11897366	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398235	1.00[CHD][hapmap]
rs16866416	1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.83[AMR][1000 genomes]
rs1864243	0.81[AMR][1000 genomes]
rs2366752	0.81[AMR][1000 genomes]
rs2366753	1.00[CHD][hapmap];0.82[GIH][hapmap]
rs28560297	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653157	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28710392	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715837	0.81[AMR][1000 genomes]
rs4893852	1.00[CHD][hapmap]
rs4893853	0.83[CHD][hapmap]
rs4894023	1.00[ASN][1000 genomes]
rs4894025	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894027	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894028	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62621236	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710877	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732060	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735083	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747122	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.83[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590037	1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap]
rs9808036	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv963939	chr2:179436201-179439832	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1000642	chr2:179438866-179503211	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
3	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:179396000-179445400	Strong transcription	Right Ventricle	heart
6	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:179409200-179439200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:179411000-179440000	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:179411000-179466000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:179411200-179440200	Weak transcription	Colonic Mucosa	Colon
11	chr2:179412000-179441000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:179413600-179440000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:179414000-179439000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:179414000-179443400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:179414200-179439200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:179414800-179471800	Weak transcription	Brain Substantia Nigra	brain
17	chr2:179417800-179441800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:179418200-179443200	Weak transcription	NHLF	lung
19	chr2:179418400-179439000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:179418400-179450200	Strong transcription	HSMMtube	muscle
21	chr2:179424000-179442200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:179424200-179442400	Strong transcription	Ovary	ovary
23	chr2:179424600-179443000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:179424800-179443000	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr2:179424800-179445200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:179425800-179440400	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr2:179425800-179446800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:179426200-179442200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr2:179427800-179443800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:179428000-179442200	Strong transcription	Liver	Liver
31	chr2:179428200-179439000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:179428400-179443800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:179428400-179478600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:179428600-179440000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:179429200-179439400	Genic enhancers	Fetal Heart	heart
36	chr2:179429400-179448400	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:179429800-179439800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:179429800-179441800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:179430600-179439000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:179430800-179480000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:179431800-179440000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:179431800-179441400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:179432400-179439000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:179433200-179440600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:179433400-179439400	Weak transcription	Thymus	Thymus
46	chr2:179433400-179443200	Weak transcription	Fetal Kidney	kidney
47	chr2:179434000-179439200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:179434200-179439000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:179434800-179440600	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr2:179434800-179440800	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links