Variant report

Variant	rs5753601
Chromosome Location	chr22:31798259-31798260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31738670..31747056-chr22:31790500..31799012,36	MCF-7	breast:
2	chr22:31737798..31746418-chr22:31793074..31801662,34	MCF-7	breast:
3	chr22:31795219..31797179-chr22:31797519..31799977,2	K562	blood:
4	chr22:31796576..31798824-chr22:32026967..32029510,2	K562	blood:

Variant related genes	Relation type
ENSG00000213888	Chromatin interaction
ENSG00000185721	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1001599	0.92[EUR][1000 genomes]
rs1034588	0.95[CEU][hapmap]
rs13054220	0.82[EUR][1000 genomes]
rs13057504	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13158	0.95[CEU][hapmap]
rs1858821	0.95[CEU][hapmap]
rs2040533	0.95[CEU][hapmap]
rs2073857	0.95[CEU][hapmap]
rs2078803	0.95[CEU][hapmap]
rs2106294	0.95[CEU][hapmap]
rs2228619	0.95[CEU][hapmap]
rs2273249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2273251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2283879	0.95[CEU][hapmap]
rs2413035	0.95[CEU][hapmap]
rs2899164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34545960	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141404	0.95[CEU][hapmap]
rs4603880	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4820043	0.95[CEU][hapmap]
rs4820955	0.95[CEU][hapmap]
rs4820963	0.95[CEU][hapmap]
rs5749265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749267	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749268	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749270	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749286	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5749298	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5753521	0.95[CEU][hapmap]
rs5753543	0.95[CEU][hapmap]
rs5753597	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753609	0.95[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs5753610	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5753612	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753613	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753615	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753618	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs5753621	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753628	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5753631	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5753632	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs5753638	0.83[CHB][hapmap]
rs5753639	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs5753659	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5753669	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5753671	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs5753698	0.80[CEU][hapmap]
rs5994394	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997969	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324184	0.80[EUR][1000 genomes]
rs714909	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs715510	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs7284622	0.82[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7285619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7287267	0.86[EUR][1000 genomes]
rs7293171	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs737684	0.95[CEU][hapmap]
rs737887	0.95[CEU][hapmap]
rs737888	0.95[CEU][hapmap]
rs738657	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8138596	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8139625	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8141150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606830	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9606831	0.86[EUR][1000 genomes]
rs9606839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9606843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9606848	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9609254	0.84[EUR][1000 genomes]
rs9609257	0.83[EUR][1000 genomes]
rs9609264	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9609265	0.86[EUR][1000 genomes]
rs9609266	0.85[EUR][1000 genomes]
rs9609267	0.87[EUR][1000 genomes]
rs9609268	0.89[EUR][1000 genomes]
rs9609276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609277	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609286	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9609296	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9609297	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9609304	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9609329	0.82[CEU][hapmap]

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	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5753601	SFI1	cis	Thyroid	GTEx
rs5753601	DRG1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31796400-31799000	Weak transcription	Aorta	Aorta
2	chr22:31796400-31803000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:31796600-31798600	Weak transcription	Ovary	ovary
4	chr22:31796600-31799400	Weak transcription	Fetal Brain Male	brain
5	chr22:31796600-31821200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:31796600-31830000	Weak transcription	Stomach Mucosa	stomach
7	chr22:31796800-31798600	Weak transcription	Brain Anterior Caudate	brain
8	chr22:31796800-31798600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr22:31796800-31798600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:31796800-31798600	Weak transcription	Fetal Lung	lung
11	chr22:31796800-31798600	Weak transcription	Lung	lung
12	chr22:31796800-31798600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:31796800-31798600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr22:31796800-31798600	Weak transcription	Thymus	Thymus
15	chr22:31796800-31798600	Weak transcription	Spleen	Spleen
16	chr22:31796800-31798600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr22:31796800-31798800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr22:31796800-31798800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:31796800-31798800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr22:31796800-31798800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr22:31796800-31799000	Weak transcription	Small Intestine	intestine
22	chr22:31796800-31799200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr22:31796800-31799600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr22:31796800-31802600	Weak transcription	Brain Substantia Nigra	brain
25	chr22:31796800-31803000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:31796800-31803000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:31796800-31804400	Weak transcription	Colonic Mucosa	Colon
28	chr22:31796800-31805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:31796800-31806600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr22:31796800-31807000	Weak transcription	Fetal Kidney	kidney
31	chr22:31796800-31807000	Weak transcription	A549	lung
32	chr22:31796800-31815800	Weak transcription	Psoas Muscle	Psoas
33	chr22:31796800-31822400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr22:31796800-31835600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr22:31797000-31798600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr22:31797000-31798600	Weak transcription	NHLF	lung
37	chr22:31797000-31798800	Weak transcription	Brain Hippocampus Middle	brain
38	chr22:31797000-31798800	Weak transcription	HSMMtube	muscle
39	chr22:31797000-31799000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr22:31797000-31799000	Weak transcription	Right Ventricle	heart
41	chr22:31797000-31801000	Strong transcription	Fetal Brain Female	brain
42	chr22:31797000-31801200	Weak transcription	HMEC	breast
43	chr22:31797000-31807000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr22:31797000-31812800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr22:31797000-31832000	Strong transcription	Fetal Muscle Leg	muscle
46	chr22:31797000-31836600	Strong transcription	Placenta	Placenta
47	chr22:31797000-31884400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:31797000-31884400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr22:31797200-31798400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr22:31797200-31798400	Weak transcription	GM12878-XiMat	blood

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