Variant report

Variant	rs2141368
Chromosome Location	chr9:94609451-94609452
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94599805..94602377-chr9:94607458..94609463,2	K562	blood:
2	chr9:94549725..94552292-chr9:94608057..94610041,2	K562	blood:
3	chr9:94597584..94599500-chr9:94607793..94610758,2	K562	blood:
4	chr9:94600587..94602440-chr9:94606824..94609770,3	K562	blood:
5	chr9:94602829..94605124-chr9:94607630..94609855,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10992124	0.91[TSI][hapmap]
rs10992128	0.82[EUR][1000 genomes]
rs10992129	0.82[EUR][1000 genomes]
rs10992130	0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10992132	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs10992137	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11789973	0.84[TSI][hapmap]
rs12552292	0.81[EUR][1000 genomes]
rs12683797	0.80[TSI][hapmap]
rs1534531	0.84[EUR][1000 genomes]
rs1534535	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16907887	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1881387	0.93[TSI][hapmap]
rs1881392	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2841691	0.83[EUR][1000 genomes]
rs4639579	0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4744105	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs4744110	0.90[TSI][hapmap]
rs56088447	0.80[EUR][1000 genomes]
rs62564597	0.81[EUR][1000 genomes]
rs62564599	0.80[EUR][1000 genomes]
rs6479376	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7039406	0.80[EUR][1000 genomes]
rs7855417	0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7863061	0.82[EUR][1000 genomes]
rs7867707	0.97[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv6614	chr9:94571349-94610085	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2141368	SPTLC1	cis	parietal	SCAN
rs2141368	BARX1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94594600-94610800	Enhancers	Fetal Thymus	thymus
2	chr9:94601800-94618400	Weak transcription	K562	blood
3	chr9:94602800-94611200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:94602800-94611600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:94604800-94610200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:94605600-94609600	Weak transcription	Spleen	Spleen
7	chr9:94606600-94609800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:94606600-94616600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:94606800-94609600	Weak transcription	Primary T cells from cord blood	blood
10	chr9:94606800-94609600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:94606800-94609800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:94606800-94609800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:94606800-94615000	Weak transcription	Right Atrium	heart
14	chr9:94606800-94619600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:94607000-94609600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:94607000-94609600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:94607000-94609800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:94607000-94609800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:94607000-94609800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:94607000-94610200	Weak transcription	Fetal Brain Male	brain
21	chr9:94607200-94610000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:94607200-94610200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:94607200-94619600	Weak transcription	Fetal Intestine Large	intestine
24	chr9:94607400-94609600	Weak transcription	NHLF	lung
25	chr9:94607600-94609600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:94607600-94609800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:94607600-94619600	Weak transcription	Fetal Intestine Small	intestine
28	chr9:94607800-94609600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:94607800-94609600	Weak transcription	Fetal Lung	lung
30	chr9:94607800-94609800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:94607800-94609800	Weak transcription	Ovary	ovary
32	chr9:94607800-94609800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:94608000-94609600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:94608200-94610200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:94608400-94609600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:94608400-94619000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:94609000-94610000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:94609000-94614400	Weak transcription	Fetal Heart	heart
39	chr9:94609200-94609600	Enhancers	Colon Smooth Muscle	Colon
40	chr9:94609200-94610000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:94609200-94610600	Enhancers	Fetal Kidney	kidney
42	chr9:94609200-94610600	Enhancers	Fetal Stomach	stomach
43	chr9:94609200-94611400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr9:94609400-94610200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:94609400-94610400	Enhancers	Fetal Muscle Leg	muscle

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