Variant report

Variant	rs12937188
Chromosome Location	chr17:60003098-60003099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:234739283..234741876-chr17:60002012..60004485,2	MCF-7	breast:
2	chr17:60000176..60003312-chr20:45769534..45773282,12	MCF-7	breast:
3	chr17:60001676..60003229-chr20:54154330..54157112,2	MCF-7	breast:
4	chr17:60001786..60003345-chr20:45777172..45778965,3	MCF-7	breast:
5	chr17:59949335..59951629-chr17:60003040..60005036,2	MCF-7	breast:
6	chr17:59939071..59942892-chr17:60002944..60006795,10	MCF-7	breast:
7	chr17:60000185..60003336-chr20:45770698..45773254,7	MCF-7	breast:
8	chr17:60002473..60006196-chr17:60142332..60145548,5	MCF-7	breast:
9	chr17:60000286..60003395-chr20:45777062..45778970,10	MCF-7	breast:
10	chr17:60002671..60006640-chr17:60140695..60145461,16	MCF-7	breast:
11	chr17:60000293..60003347-chr17:60077585..60080426,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000202361	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10221202	0.83[ASN][1000 genomes]
rs1045196	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10512491	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12601229	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12601523	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12603627	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12603878	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs16945638	1.00[MKK][hapmap]
rs16945670	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs16945724	1.00[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16945762	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16945785	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16945823	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs1809077	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2014444	0.84[CHB][hapmap]
rs2378946	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4988340	0.81[CHD][hapmap]
rs72843732	0.84[EUR][1000 genomes]
rs72843737	0.84[EUR][1000 genomes]
rs72843738	0.84[EUR][1000 genomes]
rs72843739	0.81[EUR][1000 genomes]
rs72843746	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72843758	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72843759	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72843762	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843767	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72843769	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72843770	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs72843771	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs72843772	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72843775	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72843778	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72843782	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72843785	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72843788	0.82[EUR][1000 genomes]
rs72843791	0.82[AFR][1000 genomes]
rs753765	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8081200	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs9910451	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
3	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
4	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
5	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
6	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
8	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas
9	chr17:59975400-60004600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:59978600-60004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:59980200-60003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:59982600-60003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:59983600-60004600	Weak transcription	Spleen	Spleen
14	chr17:59984200-60003400	Weak transcription	HSMMtube	muscle
15	chr17:59985000-60004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:59989200-60003400	Weak transcription	Colon Smooth Muscle	Colon
17	chr17:59989400-60003800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:59989400-60003800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:59989400-60004400	Weak transcription	Lung	lung
20	chr17:59989600-60003600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:59989600-60003600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr17:59989600-60003600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr17:59989600-60003800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr17:59989600-60003800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr17:59989600-60003800	Weak transcription	Right Ventricle	heart
26	chr17:59989600-60003800	Weak transcription	HUVEC	blood vessel
27	chr17:59989600-60003800	Weak transcription	K562	blood
28	chr17:59989600-60003800	Weak transcription	NHLF	lung
29	chr17:59994400-60003200	Strong transcription	Fetal Muscle Leg	muscle
30	chr17:59994800-60003600	Weak transcription	Fetal Brain Male	brain
31	chr17:59995800-60003600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr17:59997200-60003600	Weak transcription	Primary B cells from cord blood	blood
33	chr17:59997200-60003800	Weak transcription	Small Intestine	intestine
34	chr17:59998400-60003800	Weak transcription	Fetal Kidney	kidney
35	chr17:59998400-60004400	Weak transcription	Esophagus	oesophagus
36	chr17:59998400-60004400	Weak transcription	Gastric	stomach
37	chr17:59998400-60004600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:59998600-60003400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr17:59998600-60003600	Weak transcription	Left Ventricle	heart
40	chr17:59998600-60004200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr17:59999200-60003800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:59999600-60003600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:59999600-60003600	Weak transcription	HSMM	muscle
44	chr17:59999600-60003600	Weak transcription	NHDF-Ad	bronchial
45	chr17:60001200-60003200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr17:60001800-60003400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr17:60001800-60003600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr17:60001800-60003600	Weak transcription	Brain Substantia Nigra	brain
49	chr17:60001800-60003800	Weak transcription	NH-A	brain
50	chr17:60002400-60003600	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links