Variant report

Variant	rs61242604
Chromosome Location	chr17:16946343-16946344
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16944536..16947207-chr17:17109103..17111480,2	MCF-7	breast:
2	chr17:16944416..16947050-chr17:16979219..16983384,3	MCF-7	breast:
3	chr17:16944952..16946961-chr17:17072835..17074607,2	K562	blood:
4	chr17:16945686..16947847-chr3:44621097..44624084,2	MCF-7	breast:
5	chr17:16917707..16920531-chr17:16944662..16947361,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260328	Chromatin interaction
ENSG00000206859	Chromatin interaction
ENSG00000179598	Chromatin interaction
ENSG00000214820	Chromatin interaction
ENSG00000133030	Chromatin interaction
ENSG00000225442	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10852844	0.89[ASN][1000 genomes]
rs11078368	0.91[ASN][1000 genomes]
rs11078371	0.91[ASN][1000 genomes]
rs11078372	0.89[ASN][1000 genomes]
rs11078373	0.80[ASN][1000 genomes]
rs11551189	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11651938	0.80[ASN][1000 genomes]
rs11652678	0.80[ASN][1000 genomes]
rs11870035	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11870422	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11870483	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11870997	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12451343	0.89[ASN][1000 genomes]
rs12601422	0.87[ASN][1000 genomes]
rs12602839	0.91[ASN][1000 genomes]
rs12603417	0.91[ASN][1000 genomes]
rs2292526	0.80[ASN][1000 genomes]
rs2292530	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2349645	0.83[ASN][1000 genomes]
rs2349648	0.92[ASN][1000 genomes]
rs28452405	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34001712	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35650871	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744131	0.81[ASN][1000 genomes]
rs3744136	0.80[ASN][1000 genomes]
rs3744137	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3744138	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3744139	0.83[ASN][1000 genomes]
rs4073688	0.87[ASN][1000 genomes]
rs4074612	0.91[ASN][1000 genomes]
rs4074819	0.80[ASN][1000 genomes]
rs4321246	0.80[ASN][1000 genomes]
rs4468683	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4589617	0.85[ASN][1000 genomes]
rs4629023	0.91[ASN][1000 genomes]
rs4641803	0.88[ASN][1000 genomes]
rs4985703	0.80[ASN][1000 genomes]
rs4985716	0.94[ASN][1000 genomes]
rs4985721	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985728	0.91[ASN][1000 genomes]
rs4985730	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985737	0.80[ASN][1000 genomes]
rs56133536	0.83[ASN][1000 genomes]
rs57729820	0.95[ASN][1000 genomes]
rs60128647	0.91[ASN][1000 genomes]
rs7212275	0.94[ASN][1000 genomes]
rs7214429	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7216677	0.80[ASN][1000 genomes]
rs73979060	0.91[ASN][1000 genomes]
rs73979078	0.91[ASN][1000 genomes]
rs8071254	0.95[ASN][1000 genomes]
rs8076273	0.89[ASN][1000 genomes]
rs8077360	0.80[ASN][1000 genomes]
rs9892695	0.89[ASN][1000 genomes]
rs9893676	0.81[ASN][1000 genomes]
rs9897510	0.81[ASN][1000 genomes]
rs9906028	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9907109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9910857	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv543231	chr17:16926227-16950644	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3355439	chr17:16944752-16947600	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	esv3341315	chr17:16945077-16947125	Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61242604	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16945000-16947000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr17:16945000-16947200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr17:16945000-16948200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr17:16945200-16946800	Active TSS	Ovary	ovary
5	chr17:16945200-16947000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:16945200-16947000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:16945200-16947000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:16945200-16947000	Active TSS	Brain Anterior Caudate	brain
9	chr17:16945200-16947000	Active TSS	Fetal Brain Female	brain
10	chr17:16945200-16947000	Active TSS	Psoas Muscle	Psoas
11	chr17:16945200-16947000	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr17:16945200-16947000	Active TSS	Small Intestine	intestine
13	chr17:16945200-16947200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr17:16945200-16947200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:16945200-16947200	Active TSS	Rectal Smooth Muscle	rectum
16	chr17:16945200-16947400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:16945200-16947400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr17:16945200-16947400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr17:16945200-16947600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:16945200-16947600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:16945200-16947600	Active TSS	Fetal Kidney	kidney
22	chr17:16945200-16947600	Active TSS	Gastric	stomach
23	chr17:16945200-16947600	Active TSS	Pancreas	Pancrea
24	chr17:16945200-16947800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr17:16945200-16948400	Active TSS	Aorta	Aorta
26	chr17:16945200-16948400	Active TSS	Esophagus	oesophagus
27	chr17:16945400-16946400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:16945400-16946400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr17:16945400-16946400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:16945400-16946400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:16945400-16946400	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr17:16945400-16946400	Active TSS	Liver	Liver
33	chr17:16945400-16946400	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr17:16945400-16946400	Weak transcription	Stomach Mucosa	stomach
35	chr17:16945400-16946400	Active TSS	K562	blood
36	chr17:16945400-16946600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr17:16945400-16946600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:16945400-16946600	Active TSS	Primary B cells from peripheral blood	blood
39	chr17:16945400-16946600	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr17:16945400-16946600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr17:16945400-16946600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr17:16945400-16946600	Active TSS	Colonic Mucosa	Colon
43	chr17:16945400-16946600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr17:16945400-16946600	Active TSS	Thymus	Thymus
45	chr17:16945400-16946600	Active TSS	Dnd41	blood
46	chr17:16945400-16946800	Active TSS	H1 Cell Line	embryonic stem cell
47	chr17:16945400-16946800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:16945400-16946800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:16945400-16946800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:16945400-16946800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links