Variant report

Variant	rs1924422
Chromosome Location	chr13:37540214-37540215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:37464935..37467748-chr13:37538803..37540415,2	MCF-7	breast:
2	chr13:37540140..37543053-chr13:37572070..37575020,3	K562	blood:
3	chr13:37540140..37543219-chr13:37571723..37575020,3	K562	blood:
4	chr13:37494193..37496576-chr13:37538034..37540636,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120699	Chromatin interaction
ENSG00000120697	Chromatin interaction
ENSG00000120693	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1199962	0.90[CEU][hapmap]
rs1199963	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1199974	0.90[CEU][hapmap]
rs1199981	0.90[CEU][hapmap]
rs1199982	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs1199983	0.90[CEU][hapmap]
rs1199984	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs12865199	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1543738	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs1764483	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs1924419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1924420	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1924421	0.84[EUR][1000 genomes]
rs1937761	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2093817	0.90[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap]
rs2147169	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs2181787	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181788	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2186157	0.97[EUR][1000 genomes]
rs2323165	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2769543	0.80[CEU][hapmap]
rs2785620	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4291799	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs4624036	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs483304	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4941854	1.00[CEU][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs4941855	0.96[EUR][1000 genomes]
rs4941856	1.00[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs4943441	0.90[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs568992	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs587505	0.81[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs647421	0.93[AMR][1000 genomes]
rs6563506	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs6563507	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs6563508	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs675108	0.82[CEU][hapmap]
rs688280	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs71432622	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7317750	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs7321129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7329314	0.97[EUR][1000 genomes]
rs7334233	0.99[EUR][1000 genomes]
rs7338929	1.00[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs7982674	0.99[EUR][1000 genomes]
rs7983986	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs7984730	0.94[EUR][1000 genomes]
rs7989205	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs7989380	0.90[CEU][hapmap]
rs7991057	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7991181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7997310	0.90[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap]
rs9315458	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9315459	0.99[EUR][1000 genomes]
rs9531998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532002	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9532005	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs9547705	0.82[AMR][1000 genomes]
rs9547707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9547712	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9547715	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs9547717	0.91[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs9547718	1.00[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs9576153	0.99[EUR][1000 genomes]
rs9576154	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9594181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9603121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1924422	SUPT20H	cis	Whole Blood	GTEx
rs1924422	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
3	chr13:37521400-37542800	Weak transcription	A549	lung
4	chr13:37522600-37541000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr13:37522600-37548800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:37522800-37547000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:37523000-37545600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr13:37523200-37558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
10	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr13:37524800-37546400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:37525000-37560800	Weak transcription	Fetal Heart	heart
13	chr13:37525600-37544800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:37526600-37556200	Weak transcription	Brain Angular Gyrus	brain
15	chr13:37526800-37559400	Weak transcription	Hela-S3	cervix
16	chr13:37528600-37541800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr13:37528800-37546200	Strong transcription	Fetal Thymus	thymus
18	chr13:37529400-37546800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr13:37529400-37558200	Weak transcription	Gastric	stomach
20	chr13:37529600-37555600	Weak transcription	Stomach Mucosa	stomach
21	chr13:37530600-37545600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr13:37531800-37540800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:37531800-37541600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr13:37531800-37570000	Strong transcription	Dnd41	blood
25	chr13:37532000-37546000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr13:37532400-37545800	Strong transcription	Liver	Liver
27	chr13:37532400-37546200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr13:37532800-37540400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr13:37533000-37546400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:37533400-37543400	Strong transcription	Primary B cells from cord blood	blood
31	chr13:37533400-37545400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:37533400-37546200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr13:37534000-37545600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr13:37534600-37540400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr13:37534600-37541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:37534600-37541000	Strong transcription	Fetal Stomach	stomach
37	chr13:37534600-37541200	Strong transcription	Fetal Muscle Leg	muscle
38	chr13:37534600-37541400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:37534800-37541800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr13:37534800-37543400	Strong transcription	Fetal Intestine Large	intestine
41	chr13:37534800-37546000	Strong transcription	Placenta	Placenta
42	chr13:37535000-37545800	Strong transcription	Adipose Nuclei	Adipose
43	chr13:37535200-37553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr13:37535400-37540400	Strong transcription	GM12878-XiMat	blood
45	chr13:37535400-37549600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr13:37536000-37545400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr13:37536400-37546400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr13:37536600-37540400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:37536600-37540800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:37536600-37543200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links