Variant report

Variant	rs2542175
Chromosome Location	chr18:12726782-12726783
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	chr18:12725367..12727823-chr18:12887215..12889210,2	K562	blood:
2	chr18:12726771..12727633-chr18:12766775..12767717,3	MCF-7	breast:
3	chr18:12726736..12727393-chr18:12846308..12846890,2	MCF-7	breast:
4	chr18:12726304..12729223-chr18:12948825..12951791,2	K562	blood:
5	chr18:12689725..12692648-chr18:12725870..12727791,2	K562	blood:
6	chr18:12726635..12727970-chr18:12934143..12935576,12	K562	blood:
7	chr18:12725757..12728002-chr18:12765870..12768020,2	K562	blood:
8	chr18:12391605..12392308-chr18:12726671..12727207,2	K562	blood:
9	chr18:12720684..12722477-chr18:12725807..12728558,2	MCF-7	breast:

No data

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11080593	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11663219	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11663226	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11663260	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1539813	0.93[CHB][hapmap]
rs16939680	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs1893212	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs1893213	0.87[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs2249830	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs2542172	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs2542174	0.93[CHB][hapmap]
rs2542176	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542177	0.82[ASN][1000 genomes]
rs2847254	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796966	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs507868	0.93[CHB][hapmap]
rs8086774	0.93[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
9	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
10	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2542175	TUBB6	cis	cerebellum	SCAN
rs2542175	C22orf33	trans	cerebellum	SCAN
rs2542175	RALBP1	cis	cerebellum	SCAN
rs2542175	SPIRE1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12704200-12726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:12704800-12727200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:12704800-12727800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:12705000-12728600	Weak transcription	Stomach Mucosa	stomach
5	chr18:12705400-12727200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr18:12705600-12727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr18:12705600-12727200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr18:12705600-12727200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr18:12705600-12727200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr18:12705800-12727000	Strong transcription	Placenta	Placenta
11	chr18:12705800-12727200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr18:12705800-12727200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:12705800-12727200	Strong transcription	Fetal Muscle Leg	muscle
14	chr18:12706000-12727000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr18:12706000-12727200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:12706200-12726800	Strong transcription	Fetal Intestine Large	intestine
17	chr18:12706200-12727200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr18:12706200-12727200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr18:12706400-12727000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr18:12706400-12727000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr18:12706400-12727200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr18:12706600-12727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr18:12706600-12727200	Strong transcription	Adipose Nuclei	Adipose
24	chr18:12706800-12727000	Strong transcription	Dnd41	blood
25	chr18:12708600-12726800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr18:12709200-12726800	Strong transcription	Osteobl	bone
27	chr18:12710200-12727000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr18:12710200-12727200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr18:12710200-12727200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:12712600-12727000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr18:12712800-12727200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr18:12713800-12726800	Weak transcription	Fetal Brain Male	brain
33	chr18:12714400-12726800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr18:12714600-12728800	Weak transcription	Esophagus	oesophagus
35	chr18:12715600-12727000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr18:12716400-12726800	Strong transcription	GM12878-XiMat	blood
37	chr18:12717000-12727200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr18:12717200-12727000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr18:12717200-12727200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr18:12717400-12727200	Strong transcription	Left Ventricle	heart
41	chr18:12717600-12727200	Strong transcription	Fetal Lung	lung
42	chr18:12718400-12727200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr18:12718600-12727200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:12719000-12727800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr18:12720000-12727200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr18:12720000-12727200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr18:12720600-12727800	Strong transcription	HUVEC	blood vessel
48	chr18:12721800-12727200	Strong transcription	Primary B cells from cord blood	blood
49	chr18:12721800-12728200	Strong transcription	HSMM	muscle
50	chr18:12722000-12726800	Strong transcription	HMEC	breast

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