Variant report

Variant	rs16952071
Chromosome Location	chr13:97986448-97986449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:97984606..97986833-chr13:97996758..97998776,2	MCF-7	breast:
2	chr13:97985220..97987596-chr13:97990645..97993198,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1463791	0.83[LWK][hapmap]
rs1553012	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs17190203	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs17190210	0.91[EUR][1000 genomes]
rs17268915	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17268922	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1974085	0.84[TSI][hapmap]
rs2220971	1.00[CEU][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs3825422	1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs4578507	0.83[CEU][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4771992	0.84[TSI][hapmap]
rs55684003	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59036109	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59512800	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59788734	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60452878	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60805672	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72637476	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7318821	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7327210	0.81[EUR][1000 genomes]
rs7333641	0.95[CEU][hapmap];0.85[GIH][hapmap]
rs7358848	0.88[CEU][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8000986	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs9300404	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9554389	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9556701	0.81[LWK][hapmap];0.82[YRI][hapmap]
rs9556704	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9582124	0.91[CEU][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9584547	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9584549	0.83[CEU][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9584552	0.81[LWK][hapmap]
rs9584554	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9584555	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9584556	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9584559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9584560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9584564	0.90[EUR][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	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16952071	SLC35F2	trans	cerebellum	SCAN
rs16952071	MBNL2	cis	brain	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97925800-97987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr13:97942800-97995200	Weak transcription	Thymus	Thymus
3	chr13:97955000-97987000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr13:97955200-97986800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:97959400-97988800	Weak transcription	Fetal Intestine Large	intestine
6	chr13:97961400-97987200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:97962000-97991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:97965600-97988800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr13:97965800-97987200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr13:97967400-97991400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:97969600-97987200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr13:97969800-97986600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr13:97971600-97991400	Weak transcription	Stomach Mucosa	stomach
14	chr13:97971800-97987200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:97971800-97987600	Weak transcription	Fetal Intestine Small	intestine
16	chr13:97971800-97987800	Weak transcription	Colonic Mucosa	Colon
17	chr13:97971800-97991800	Weak transcription	Small Intestine	intestine
18	chr13:97972000-97987200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr13:97976200-97990400	Weak transcription	Fetal Brain Male	brain
20	chr13:97977400-97987000	Weak transcription	Hela-S3	cervix
21	chr13:97978200-97987000	Enhancers	Colon Smooth Muscle	Colon
22	chr13:97979800-97986800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:97980000-97989000	Enhancers	Brain Hippocampus Middle	brain
24	chr13:97980600-97988000	Enhancers	Brain Substantia Nigra	brain
25	chr13:97980800-97987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:97980800-97987600	Weak transcription	NHEK	skin
27	chr13:97980800-97988600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr13:97980800-97988600	Weak transcription	Fetal Thymus	thymus
29	chr13:97980800-97990400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:97980800-97991800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr13:97981000-97986600	Weak transcription	Placenta	Placenta
32	chr13:97981000-97988200	Weak transcription	Osteobl	bone
33	chr13:97981000-97989200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr13:97981000-97991400	Weak transcription	HMEC	breast
35	chr13:97981000-97998800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:97981200-97987200	Weak transcription	A549	lung
37	chr13:97981200-97991400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr13:97981800-97987200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:97981800-97987200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:97981800-97987200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:97981800-97987600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:97981800-97987600	Weak transcription	NH-A	brain
43	chr13:97982000-97989000	Weak transcription	HSMMtube	muscle
44	chr13:97982000-97991400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr13:97982000-98002200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr13:97982000-98009000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:97982200-97988000	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr13:97982200-97988600	Weak transcription	Gastric	stomach
49	chr13:97982200-97990400	Weak transcription	Spleen	Spleen
50	chr13:97982200-97991200	Weak transcription	Fetal Kidney	kidney

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