Variant report

Variant	rs10195153
Chromosome Location	chr2:20551993-20551994
allele	A/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	PML	chr2:20549570-20552013	GM12878	blood:	n/a	n/a
2	GATA3	chr2:20551766-20552248	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr2:20549406-20552284	GM12891	blood:	n/a	n/a
4	MXI1	chr2:20549160-20551997	GM12878	blood:	n/a	n/a
5	REST	chr2:20549719-20552691	H1-neurons	neurons:	n/a	chr2:20551488-20551498 chr2:20550584-20550597 chr2:20551490-20551503 chr2:20550778-20550791
6	POLR2A	chr2:20551802-20552395	H1-neurons	neurons:	n/a	n/a
7	KAP1	chr2:20550744-20552344	HEK293	kidney:	n/a	n/a
8	POLR2A	chr2:20549870-20552004	GM19099	blood:	n/a	n/a
9	POLR2A	chr2:20549605-20552127	SK-N-MC	brain:	n/a	n/a
10	GATA2	chr2:20551914-20552302	SH-SY5Y	brain:	n/a	n/a
11	POLR2A	chr2:20549870-20552194	GM12892	blood:	n/a	n/a
12	POLR2A	chr2:20549436-20552270	GM12878	blood:	n/a	n/a
13	RCOR1	chr2:20551877-20552267	K562	blood:	n/a	n/a
14	MXI1	chr2:20547982-20554007	SK-N-SH	brain:	n/a	chr2:20552662-20552671
15	POLR2A	chr2:20549643-20552073	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20550911..20553369-chr2:20646204..20648737,2	K562	blood:
2	chr2:20550750..20552615-chr2:21021758..21023805,2	K562	blood:
3	chr12:48572524..48575406-chr2:20550361..20552479,2	MCF-7	breast:
4	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
5	chr2:20523318..20529381-chr2:20544822..20552572,11	K562	blood:
6	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:
7	chr2:20549505..20552081-chr2:20849266..20851365,2	MCF-7	breast:

Variant related genes	Relation type
PUM2	TF binding region
ENSG00000055917	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000118961	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10153828	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs10167509	1.00[ASN][1000 genomes]
rs10168575	1.00[ASN][1000 genomes]
rs10170538	1.00[ASN][1000 genomes]
rs10171025	1.00[ASN][1000 genomes]
rs10171861	1.00[ASN][1000 genomes]
rs10172088	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10173098	1.00[ASN][1000 genomes]
rs10174768	1.00[ASN][1000 genomes]
rs10176257	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177428	1.00[ASN][1000 genomes]
rs10178561	1.00[ASN][1000 genomes]
rs10179429	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs10182156	1.00[ASN][1000 genomes]
rs10182228	1.00[ASN][1000 genomes]
rs10182834	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs10184976	1.00[ASN][1000 genomes]
rs10189781	1.00[ASN][1000 genomes]
rs10193751	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap]
rs10194789	1.00[ASN][1000 genomes]
rs10195817	1.00[ASN][1000 genomes]
rs10197941	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10198897	1.00[ASN][1000 genomes]
rs10204489	1.00[ASN][1000 genomes]
rs10207798	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10208668	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390701	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13391140	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs13398963	1.00[ASN][1000 genomes]
rs13409830	1.00[ASN][1000 genomes]
rs13412971	1.00[ASN][1000 genomes]
rs13421653	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425933	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426989	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs13429586	1.00[ASN][1000 genomes]
rs16987553	0.89[ASW][hapmap];0.89[LWK][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes]
rs28732678	1.00[ASN][1000 genomes]
rs4427977	0.89[ASW][hapmap];0.89[LWK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs55904622	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56337814	1.00[EUR][1000 genomes]
rs57065686	1.00[ASN][1000 genomes]
rs57459161	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58774661	1.00[ASN][1000 genomes]
rs59901600	1.00[ASN][1000 genomes]
rs60984167	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62111434	1.00[ASN][1000 genomes]
rs62111435	1.00[ASN][1000 genomes]
rs62111436	1.00[ASN][1000 genomes]
rs62111437	1.00[ASN][1000 genomes]
rs62111439	1.00[ASN][1000 genomes]
rs62123438	1.00[ASN][1000 genomes]
rs62123439	1.00[ASN][1000 genomes]
rs62123441	1.00[ASN][1000 genomes]
rs62123443	1.00[ASN][1000 genomes]
rs62123444	1.00[ASN][1000 genomes]
rs62123446	1.00[ASN][1000 genomes]
rs62123448	1.00[ASN][1000 genomes]
rs62123450	1.00[ASN][1000 genomes]
rs62123453	1.00[ASN][1000 genomes]
rs62123454	1.00[ASN][1000 genomes]
rs62123455	1.00[ASN][1000 genomes]
rs62123456	1.00[ASN][1000 genomes]
rs62123458	1.00[ASN][1000 genomes]
rs62124592	1.00[ASN][1000 genomes]
rs62124596	1.00[ASN][1000 genomes]
rs62124597	1.00[ASN][1000 genomes]
rs62124598	1.00[ASN][1000 genomes]
rs62124599	1.00[ASN][1000 genomes]
rs62124600	1.00[ASN][1000 genomes]
rs62124601	1.00[ASN][1000 genomes]
rs62124602	1.00[ASN][1000 genomes]
rs62124604	1.00[ASN][1000 genomes]
rs6709651	0.83[AMR][1000 genomes]
rs6715475	1.00[ASN][1000 genomes]
rs6744963	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs73214391	1.00[ASN][1000 genomes]
rs73214393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73216207	1.00[ASN][1000 genomes]
rs73216223	1.00[ASN][1000 genomes]
rs73216230	1.00[ASN][1000 genomes]
rs73216236	1.00[ASN][1000 genomes]
rs73218112	1.00[ASN][1000 genomes]
rs73218122	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73218124	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73218129	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73218135	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741189	1.00[CEU][hapmap]
rs7565347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7589484	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759220	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759221	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653390	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808229	1.00[ASN][1000 genomes]

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	esv3423314	chr2:20549496-20552044	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10195153	DHDH	trans	brain	seeQTL
rs10195153	HSPA6	trans	brain	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20549000-20552000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:20550800-20552200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:20550800-20552200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr2:20550800-20552800	Flanking Active TSS	Fetal Brain Male	brain
5	chr2:20551000-20552000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:20551000-20552000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr2:20551000-20552000	Flanking Bivalent TSS/Enh	HepG2	liver
8	chr2:20551000-20552000	Flanking Active TSS	NHEK	skin
9	chr2:20551000-20552200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:20551000-20552200	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr2:20551000-20552200	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr2:20551000-20552400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:20551000-20552800	Flanking Active TSS	GM12878-XiMat	blood
14	chr2:20551000-20554000	Flanking Active TSS	Fetal Brain Female	brain
15	chr2:20551200-20552000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr2:20551200-20552000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr2:20551200-20552000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr2:20551200-20552000	Flanking Active TSS	Hela-S3	cervix
19	chr2:20551200-20552200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20551200-20552200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr2:20551200-20552200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr2:20551200-20552400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr2:20551200-20552600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr2:20551400-20552200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:20551400-20552200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:20551400-20552200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:20551400-20552200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr2:20551400-20552200	Enhancers	Left Ventricle	heart
29	chr2:20551400-20552200	Enhancers	Lung	lung
30	chr2:20551400-20552400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:20551400-20552400	Flanking Active TSS	Dnd41	blood
32	chr2:20551400-20552600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:20551600-20552000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:20551600-20552000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:20551600-20552000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:20551600-20552000	Flanking Active TSS	Colonic Mucosa	Colon
37	chr2:20551600-20552000	Weak transcription	Esophagus	oesophagus
38	chr2:20551600-20552000	Enhancers	Fetal Kidney	kidney
39	chr2:20551600-20552000	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:20551600-20552000	Enhancers	Small Intestine	intestine
41	chr2:20551600-20552000	Enhancers	HUVEC	blood vessel
42	chr2:20551600-20552200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:20551600-20552200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:20551600-20552200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:20551600-20552200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:20551600-20552200	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr2:20551600-20552200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:20551600-20552200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:20551600-20552200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:20551600-20552200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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