Variant report

Variant	rs12601229
Chromosome Location	chr17:59986993-59986994
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59985102..59987364-chr20:45770274..45772515,2	MCF-7	breast:
2	chr17:59985366..59987278-chr17:60080695..60083586,2	MCF-7	breast:
3	chr17:59979529..59987949-chr20:54150484..54157842,44	MCF-7	breast:
4	chr17:59976105..59981042-chr17:59982250..59988291,12	MCF-7	breast:
5	chr17:59984959..59987360-chr17:60080196..60082621,4	MCF-7	breast:
6	chr17:56708368..56709944-chr17:59985998..59988197,2	MCF-7	breast:
7	chr17:59978593..59987926-chr20:54150517..54157312,46	MCF-7	breast:
8	chr17:59981242..59982968-chr17:59986107..59988838,2	K562	blood:
9	chr17:59984827..59990978-chr17:60003230..60006260,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000242398	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1045196	1.00[AFR][1000 genomes]
rs10512491	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12601523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603627	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12603878	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12937188	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16945670	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16945724	1.00[AFR][1000 genomes]
rs16945762	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16945785	1.00[AFR][1000 genomes]
rs1809077	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2378946	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72843732	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843737	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72843738	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843739	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72843746	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72843758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843759	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72843762	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72843767	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72843769	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72843770	1.00[AFR][1000 genomes]
rs72843771	1.00[AFR][1000 genomes]
rs72843772	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72843775	0.80[EUR][1000 genomes]
rs72843778	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72843782	1.00[AFR][1000 genomes]
rs72843785	1.00[AFR][1000 genomes]
rs72843791	0.82[AFR][1000 genomes]
rs753765	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8081200	0.98[EUR][1000 genomes];0.94[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	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
5	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
6	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
7	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:59951400-59992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:59951600-59989600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:59958000-59987600	Weak transcription	Esophagus	oesophagus
14	chr17:59959000-59996800	Weak transcription	Gastric	stomach
15	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
16	chr17:59963400-59989600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:59963800-59989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas
19	chr17:59966200-59987600	Weak transcription	Ovary	ovary
20	chr17:59966200-59998000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:59967600-59987000	Weak transcription	Fetal Brain Male	brain
22	chr17:59967600-59988400	Weak transcription	K562	blood
23	chr17:59974200-59989600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr17:59974200-59993000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:59974400-59989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:59974800-59989400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr17:59975000-59989400	Strong transcription	Fetal Thymus	thymus
28	chr17:59975400-59991800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:59975400-60004600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:59975600-59989600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:59975600-59991000	Strong transcription	Fetal Stomach	stomach
32	chr17:59976200-59992400	Strong transcription	HepG2	liver
33	chr17:59977200-59989600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr17:59977400-59989600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr17:59977400-59989600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:59978400-59989600	Strong transcription	Dnd41	blood
37	chr17:59978600-60004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:59979000-59989600	Strong transcription	Primary T cells from cord blood	blood
39	chr17:59979000-59989600	Strong transcription	Liver	Liver
40	chr17:59979000-59989600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr17:59979400-59989200	Strong transcription	HSMM	muscle
42	chr17:59980200-60003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:59980800-59989400	Strong transcription	Fetal Brain Female	brain
44	chr17:59981400-59987000	Weak transcription	HMEC	breast
45	chr17:59981600-59989600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr17:59982000-59987000	Weak transcription	Brain Angular Gyrus	brain
47	chr17:59982000-59988800	Weak transcription	NHDF-Ad	bronchial
48	chr17:59982000-59992400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr17:59982200-59987000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr17:59982200-59989600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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