Variant report

Variant	rs1275179
Chromosome Location	chr13:30919681-30919682
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	chr13:30880965..30883044-chr13:30919310..30921357,2	MCF-7	breast:
2	chr13:30912562..30914754-chr13:30916773..30919801,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KATNAL1-3	chr13:30919570-30919863	XLOC_010556
2	lnc-USPL1-2	chr13:30918809-30921304	NONHSAT032785

Variant related genes	Relation type
ENSG00000102781	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11616886	0.80[EUR][1000 genomes]
rs1275180	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1275181	0.84[EUR][1000 genomes]
rs1291150	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13378210	0.90[CEU][hapmap];0.80[AMR][1000 genomes]
rs1621497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1754937	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17589894	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs200507	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200508	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200509	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs202102	0.90[TSI][hapmap]
rs202103	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs202108	0.83[ASN][1000 genomes]
rs2077011	0.87[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2149852	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2149853	0.85[EUR][1000 genomes]
rs2183284	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2185009	0.84[EUR][1000 genomes]
rs2388536	0.85[EUR][1000 genomes]
rs55825913	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs595756	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs657160	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7997259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9285072	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9578163	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9579556	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9579558	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530602	chr13:30911025-31404272	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv455853	chr13:30911531-30951514	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv561394	chr13:30911531-30951514	Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1275179	KATNAL1	cis	cerebellum	SCAN
rs1275179	RASL11A	cis	parietal	SCAN
rs1275179	PDX1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30909000-30919800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr13:30910000-30920600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr13:30915400-30920000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr13:30915400-30920200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr13:30915400-30920600	Weak transcription	Right Atrium	heart
6	chr13:30915400-30921600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:30916600-30920600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr13:30917000-30926800	Weak transcription	Aorta	Aorta
9	chr13:30917200-30920200	Weak transcription	HMEC	breast
10	chr13:30917200-30920400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr13:30917200-30920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:30917200-30920600	Weak transcription	NHEK	skin
13	chr13:30917400-30920400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr13:30917600-30920200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr13:30917600-30920400	Weak transcription	Colon Smooth Muscle	Colon
16	chr13:30917800-30920400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:30918000-30920400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:30918600-30920400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr13:30919000-30920400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr13:30919000-30920400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:30919000-30920400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr13:30919000-30920600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr13:30919000-30922200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr13:30919000-30922200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr13:30919200-30919800	Strong transcription	Fetal Thymus	thymus
26	chr13:30919200-30920200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr13:30919200-30920600	Enhancers	Spleen	Spleen
28	chr13:30919200-30922200	Enhancers	Primary B cells from peripheral blood	blood
29	chr13:30919200-30922800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:30919200-30922800	Enhancers	Dnd41	blood
31	chr13:30919400-30920000	Genic enhancers	Thymus	Thymus
32	chr13:30919400-30920400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr13:30919400-30922200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr13:30919600-30919800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr13:30919600-30920400	Enhancers	Primary B cells from cord blood	blood
36	chr13:30919600-30920400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr13:30919600-30920800	Enhancers	Esophagus	oesophagus

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