Variant report

Variant	rs2012
Chromosome Location	chr17:38154084-38154085
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38139073..38144871-chr17:38149897..38154984,7	K562	blood:
2	chr17:38152599..38155402-chr17:38158806..38161805,3	K562	blood:
3	chr17:38152976..38154813-chr17:38189662..38192619,2	K562	blood:
4	chr17:38148349..38150160-chr17:38151852..38154932,3	K562	blood:

Variant related genes	Relation type
ENSG00000008838	Chromatin interaction
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11078932	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555254	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs11555255	0.96[EUR][1000 genomes]
rs11654473	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11655584	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs2227316	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2827	0.94[CEU][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs36006659	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3859188	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58212353	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503529	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7217241	0.96[EUR][1000 genomes]
rs7217694	0.97[EUR][1000 genomes]
rs7222093	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7222556	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224260	0.88[CEU][hapmap];0.99[EUR][1000 genomes]
rs7225565	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8068076	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8073732	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs8080546	0.94[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894543	0.86[CEU][hapmap];0.99[EUR][1000 genomes]
rs9912981	0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913535	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9916279	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2012	PSMD3	cis	multi-tissue	Pritchard
rs2012	ENSG00000108344	cis	multi-tissue	Pritchard
rs2012	MED24	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38138600-38154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:38139200-38154800	Strong transcription	Fetal Intestine Small	intestine
3	chr17:38139400-38154400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:38139400-38155000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:38139600-38154400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr17:38139600-38154600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:38139600-38154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:38139600-38155000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:38139600-38155200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:38139600-38155400	Strong transcription	Placenta	Placenta
11	chr17:38139600-38155600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:38139600-38155600	Strong transcription	Fetal Thymus	thymus
13	chr17:38139800-38154400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr17:38139800-38154400	Strong transcription	HMEC	breast
15	chr17:38139800-38154600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr17:38139800-38154600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:38139800-38154800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr17:38139800-38155000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:38139800-38155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:38139800-38155000	Strong transcription	A549	lung
21	chr17:38139800-38155600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr17:38140000-38154200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:38140000-38154200	Strong transcription	Brain Germinal Matrix	brain
24	chr17:38140000-38154200	Strong transcription	Lung	lung
25	chr17:38140000-38154400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:38140000-38154400	Strong transcription	Right Ventricle	heart
27	chr17:38140000-38154600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:38140000-38154600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr17:38140000-38154600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr17:38140000-38154600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:38140000-38154600	Strong transcription	Brain Hippocampus Middle	brain
32	chr17:38140000-38154600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr17:38140000-38154600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:38140000-38154600	Strong transcription	Fetal Intestine Large	intestine
35	chr17:38140000-38155000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:38140000-38155000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr17:38140000-38155000	Strong transcription	Rectal Smooth Muscle	rectum
38	chr17:38140000-38155000	Strong transcription	HSMM	muscle
39	chr17:38140000-38155200	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr17:38140000-38155800	Strong transcription	Fetal Stomach	stomach
41	chr17:38140200-38154400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:38140200-38154400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr17:38140200-38154400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr17:38140200-38154400	Strong transcription	HepG2	liver
45	chr17:38140200-38155000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:38140400-38154200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr17:38140400-38154200	Strong transcription	Ovary	ovary
48	chr17:38140400-38154200	Strong transcription	Pancreas	Pancrea
49	chr17:38140400-38154400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr17:38140400-38154400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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