Variant report

Variant	rs3934886
Chromosome Location	chr17:38195495-38195496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38186756..38191531-chr17:38192826..38198444,5	K562	blood:
2	chr17:38191841..38193533-chr17:38193734..38195685,2	K562	blood:
3	chr17:38195040..38195745-chr17:38267685..38268551,2	MCF-7	breast:
4	chr17:38195054..38195831-chr17:38267591..38268173,3	MCF-7	breast:
5	chr17:38195259..38195816-chr17:38242433..38243085,2	MCF-7	breast:
6	chr17:38194833..38195774-chr17:38242417..38243342,4	K562	blood:
7	chr17:38193120..38197062-chr17:38206698..38210454,3	K562	blood:
8	chr17:38194560..38196821-chr17:38283117..38285170,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000008838	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1042657	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10852937	0.81[GIH][hapmap]
rs2071369	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2071370	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2227324	0.81[ASN][1000 genomes]
rs2227338	0.81[ASN][1000 genomes]
rs2302775	0.81[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2302778	0.84[ASN][1000 genomes]
rs6503532	0.81[ASN][1000 genomes]
rs6503534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7503939	0.84[ASN][1000 genomes]
rs8070452	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921651	0.83[GIH][hapmap]
rs9899955	0.82[ASN][1000 genomes]
rs9913632	0.88[JPT][hapmap];0.82[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3934886	MED24	cis	Muscle Skeletal	GTEx
rs3934886	KRTAP4-2	cis	parietal	SCAN
rs3934886	MED24	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38183000-38195600	Strong transcription	Primary T cells from cord blood	blood
2	chr17:38183800-38195600	Strong transcription	Fetal Thymus	thymus
3	chr17:38186600-38209800	Weak transcription	Small Intestine	intestine
4	chr17:38188800-38209400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:38189600-38206600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:38189600-38209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:38189600-38209600	Weak transcription	Psoas Muscle	Psoas
8	chr17:38190600-38209600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:38191000-38208800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:38191400-38201000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr17:38191800-38206000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr17:38192000-38209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:38192200-38206600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr17:38192200-38209400	Weak transcription	Fetal Brain Male	brain
15	chr17:38192200-38209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr17:38192400-38199000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:38192400-38209600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:38192400-38209600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:38192400-38209600	Weak transcription	Colonic Mucosa	Colon
20	chr17:38192400-38209800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:38192400-38210000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:38192600-38197400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:38192600-38197400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr17:38192600-38197600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:38192600-38197600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr17:38192600-38198200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:38192600-38198400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:38192600-38198600	Weak transcription	GM12878-XiMat	blood
29	chr17:38192600-38198800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:38192600-38198800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr17:38192600-38199200	Weak transcription	Gastric	stomach
32	chr17:38192600-38201400	Weak transcription	Lung	lung
33	chr17:38192600-38201800	Weak transcription	Fetal Brain Female	brain
34	chr17:38192600-38203200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr17:38192600-38205600	Weak transcription	Spleen	Spleen
36	chr17:38192600-38206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr17:38192600-38206600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:38192600-38208600	Weak transcription	NHEK	skin
39	chr17:38192600-38209400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr17:38192600-38209800	Weak transcription	Aorta	Aorta
41	chr17:38192800-38198800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr17:38193200-38197600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr17:38193200-38199200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:38193200-38199400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr17:38193200-38199400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr17:38193200-38203200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr17:38193200-38203200	Weak transcription	Dnd41	blood
48	chr17:38193400-38196600	Weak transcription	Fetal Intestine Large	intestine
49	chr17:38193400-38197400	Weak transcription	Primary B cells from cord blood	blood
50	chr17:38193600-38196000	Enhancers	Colon Smooth Muscle	Colon

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