Variant report

Variant	rs6678145
Chromosome Location	chr1:228684779-228684780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228663829..228665907-chr1:228683407..228685516,2	MCF-7	breast:
2	chr1:228678547..228680659-chr1:228683651..228685431,2	MCF-7	breast:
3	chr1:228684681..228686315-chr1:228686829..228688475,2	MCF-7	breast:
4	chr1:228672968..228678350-chr1:228679226..228685848,20	MCF-7	breast:
5	chr1:228674046..228678043-chr1:228684721..228686964,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10799479	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916314	0.80[CEU][hapmap]
rs10916329	0.91[EUR][1000 genomes]
rs12060006	0.86[EUR][1000 genomes]
rs12542	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12751024	1.00[CHD][hapmap]
rs1925714	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1925730	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653554	0.97[EUR][1000 genomes]
rs4653966	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653968	1.00[EUR][1000 genomes]
rs4653969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4653970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56677959	1.00[ASN][1000 genomes]
rs60633830	1.00[ASN][1000 genomes]
rs6426505	0.89[EUR][1000 genomes]
rs6665140	1.00[CHD][hapmap]
rs6669744	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555298	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
4	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
10	nsv549297	chr1:228681195-228720480	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv468305	chr1:228681195-228731677	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv549298	chr1:228681195-228731677	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6678145	RNF187	cis	cerebellum	SCAN
rs6678145	DUSP5P	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228676400-228684800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:228676400-228685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:228676400-228688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228676600-228688800	Weak transcription	HUVEC	blood vessel
5	chr1:228676800-228685600	Strong transcription	Primary T cells from cord blood	blood
6	chr1:228676800-228686000	Strong transcription	Fetal Intestine Small	intestine
7	chr1:228676800-228688400	Weak transcription	Stomach Mucosa	stomach
8	chr1:228676800-228688600	Weak transcription	Small Intestine	intestine
9	chr1:228677000-228685200	Strong transcription	Fetal Lung	lung
10	chr1:228677000-228686000	Strong transcription	Fetal Stomach	stomach
11	chr1:228677400-228685400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:228677400-228685800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:228677400-228686000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:228677600-228686000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:228677600-228686000	Strong transcription	Ovary	ovary
16	chr1:228678000-228686000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:228678200-228685000	Strong transcription	Liver	Liver
18	chr1:228678200-228686000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:228678200-228686000	Strong transcription	Lung	lung
20	chr1:228678400-228684800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:228678400-228685400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:228678400-228688600	Weak transcription	Fetal Brain Male	brain
23	chr1:228678600-228685800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:228678600-228686200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:228678600-228688400	Weak transcription	Hela-S3	cervix
26	chr1:228678800-228685200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:228678800-228685600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:228678800-228686000	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:228678800-228686200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:228678800-228687400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:228678800-228688200	Weak transcription	A549	lung
32	chr1:228678800-228688800	Weak transcription	Psoas Muscle	Psoas
33	chr1:228679000-228688600	Weak transcription	Fetal Kidney	kidney
34	chr1:228679000-228688600	Weak transcription	Right Atrium	heart
35	chr1:228679200-228688600	Weak transcription	NH-A	brain
36	chr1:228679400-228685800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:228679600-228687200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:228679600-228687400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:228679800-228686200	Strong transcription	Dnd41	blood
40	chr1:228680000-228685400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:228680200-228685800	Strong transcription	Fetal Brain Female	brain
42	chr1:228680400-228685800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:228680600-228685400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:228680600-228686000	Strong transcription	Thymus	Thymus
45	chr1:228680800-228685000	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:228680800-228685800	Strong transcription	Primary B cells from cord blood	blood
47	chr1:228681000-228685800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr1:228681200-228686000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:228681800-228688200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:228682000-228685400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links