Variant report

Variant	rs10205400
Chromosome Location	chr2:11915284-11915285
allele	A/C
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	chr2:11915241-11915782	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11902752..11905515-chr2:11914841..11917001,2	K562	blood:

Variant related genes	Relation type
LPIN1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1006538	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10169802	0.89[ASN][1000 genomes]
rs10192566	0.89[ASN][1000 genomes]
rs10205312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10207506	0.88[ASN][1000 genomes]
rs10208679	0.88[ASN][1000 genomes]
rs10209969	0.96[ASN][1000 genomes]
rs11676086	0.88[ASN][1000 genomes]
rs11693809	0.89[ASN][1000 genomes]
rs11897144	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13407101	0.94[ASN][1000 genomes]
rs13409154	0.88[ASN][1000 genomes]
rs13412852	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1469952	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17603420	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs2099597	0.84[ASN][1000 genomes]
rs2278513	0.87[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs2358041	0.98[ASN][1000 genomes]
rs2358042	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2358126	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs4076055	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4129757	0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4315495	0.88[ASN][1000 genomes]
rs62113306	0.86[ASN][1000 genomes]
rs6717910	0.88[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs6731096	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6757892	0.87[ASN][1000 genomes]
rs72773994	0.96[ASN][1000 genomes]
rs7561070	0.87[ASN][1000 genomes]
rs7595221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7607755	0.87[ASN][1000 genomes]
rs873358	0.88[ASN][1000 genomes]
rs893342	0.90[AFR][1000 genomes];0.97[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11888400-11916400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:11895000-11918200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:11900600-11918000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:11901800-11918600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:11905000-11915400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:11905200-11919000	Weak transcription	Stomach Mucosa	stomach
7	chr2:11905400-11915600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:11905400-11916600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr2:11905400-11916800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:11906000-11917400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:11906400-11924600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:11906600-11924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:11906800-11924600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:11907200-11916800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:11908000-11919000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:11908600-11917600	Strong transcription	K562	blood
17	chr2:11909000-11915600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:11909000-11919000	Strong transcription	HMEC	breast
19	chr2:11909600-11915400	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:11909600-11916600	Strong transcription	Fetal Stomach	stomach
21	chr2:11909800-11915400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:11909800-11915800	Strong transcription	Brain Hippocampus Middle	brain
23	chr2:11909800-11915800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:11910000-11915400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:11910000-11915600	Strong transcription	Fetal Thymus	thymus
26	chr2:11910000-11917400	Strong transcription	HepG2	liver
27	chr2:11910000-11918400	Strong transcription	Thymus	Thymus
28	chr2:11910200-11915600	Strong transcription	Brain Germinal Matrix	brain
29	chr2:11910200-11916400	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr2:11911000-11915600	Strong transcription	Brain Cingulate Gyrus	brain
31	chr2:11911600-11915400	Strong transcription	HSMMtube	muscle
32	chr2:11911800-11915400	Strong transcription	Brain Anterior Caudate	brain
33	chr2:11911800-11918200	Weak transcription	Small Intestine	intestine
34	chr2:11912000-11915600	Weak transcription	Hela-S3	cervix
35	chr2:11912000-11919000	Weak transcription	A549	lung
36	chr2:11912200-11915600	Weak transcription	Fetal Kidney	kidney
37	chr2:11912200-11916400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:11912400-11917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:11912400-11917400	Weak transcription	Aorta	Aorta
40	chr2:11912400-11917400	Weak transcription	Spleen	Spleen
41	chr2:11912400-11917600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:11912400-11918200	Weak transcription	Colonic Mucosa	Colon
43	chr2:11912400-11919200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:11912600-11918400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:11912600-11918400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:11912600-11920400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:11913400-11915800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:11913600-11915400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:11913600-11919000	Weak transcription	Brain Substantia Nigra	brain
50	chr2:11913800-11915400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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