Variant report

Variant	rs12188906
Chromosome Location	chr5:154171530-154171531
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:154171065-154172608	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr5:154171527-154171995	K562	blood:	n/a	n/a
3	POLR2A	chr5:154171170-154171615	K562	blood:	n/a	n/a
4	POLR2A	chr5:154171181-154172516	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
LARP1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10515727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186480	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12186610	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12187572	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187890	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12187921	1.00[CEU][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12187934	0.82[ASN][1000 genomes]
rs12187974	0.86[ASN][1000 genomes]
rs12188149	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12188498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189508	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1421813	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17096232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17116417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116433	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17116455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116534	1.00[CHB][hapmap]
rs17116638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17116669	0.82[ASN][1000 genomes]
rs2047305	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2112223	1.00[CHB][hapmap]
rs2291780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2544859	0.82[CHB][hapmap]
rs2644744	1.00[CHB][hapmap]
rs2688198	1.00[CHB][hapmap]
rs2688208	1.00[CHB][hapmap]
rs28372688	0.86[ASN][1000 genomes]
rs3776984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4452598	0.92[EUR][1000 genomes]
rs4626377	0.92[EUR][1000 genomes]
rs55692274	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56773390	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56895891	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61145644	0.82[ASN][1000 genomes]
rs6580123	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871813	0.82[ASN][1000 genomes]
rs6895588	0.82[ASN][1000 genomes]
rs6895702	0.82[ASN][1000 genomes]
rs6895741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs73806917	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807206	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807207	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807213	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73807216	0.82[ASN][1000 genomes]
rs73809507	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709899	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7716019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816718	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154164000-154173600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:154164200-154176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:154164600-154188200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:154166000-154176000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:154166400-154173200	Strong transcription	Fetal Intestine Small	intestine
6	chr5:154167000-154203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:154168000-154171600	Weak transcription	Stomach Mucosa	stomach
8	chr5:154168000-154174600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:154168200-154172800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:154168200-154173800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:154168600-154171800	Weak transcription	Fetal Heart	heart
12	chr5:154168600-154172400	Weak transcription	Psoas Muscle	Psoas
13	chr5:154169200-154172000	Strong transcription	Hela-S3	cervix
14	chr5:154169200-154204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:154169200-154204200	Strong transcription	Dnd41	blood
16	chr5:154169400-154171600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:154169400-154172400	Strong transcription	Fetal Intestine Large	intestine
18	chr5:154169400-154173200	Strong transcription	Gastric	stomach
19	chr5:154169400-154173600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:154169400-154173600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:154169400-154175000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:154169400-154175000	Strong transcription	Spleen	Spleen
23	chr5:154169400-154176400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:154169400-154176400	Strong transcription	Colonic Mucosa	Colon
25	chr5:154169400-154176400	Strong transcription	Fetal Lung	lung
26	chr5:154169400-154176600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:154169400-154176600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:154169400-154177000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:154169400-154178800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:154169400-154179200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr5:154169400-154186200	Strong transcription	Fetal Stomach	stomach
32	chr5:154169400-154188400	Strong transcription	NHEK	skin
33	chr5:154169400-154190400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr5:154169400-154191000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:154169400-154191200	Strong transcription	Primary T cells from cord blood	blood
36	chr5:154169400-154191200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:154169400-154191400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:154169400-154192600	Strong transcription	Fetal Thymus	thymus
39	chr5:154169400-154194800	Strong transcription	K562	blood
40	chr5:154169400-154198200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr5:154169400-154198400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:154169400-154198800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:154169400-154199000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr5:154169400-154199400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:154169400-154200000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:154169400-154200800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr5:154169400-154201400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:154169400-154204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:154169400-154204200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:154169400-154204200	Strong transcription	Duodenum Mucosa	Duodenum

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