Variant report

Variant	rs1048348
Chromosome Location	chr15:49936238-49936239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49934440..49937340-chr15:49937772..49940035,3	MCF-7	breast:
2	chr15:49936169..49939153-chr15:49946646..49948297,2	K562	blood:
3	chr15:49934468..49937629-chr15:49939008..49941773,3	K562	blood:
4	chr15:49932896..49934447-chr15:49935029..49936774,2	MCF-7	breast:
5	chr15:49935570..49938221-chr15:49938905..49941859,4	K562	blood:
6	chr15:49928084..49930382-chr15:49935420..49939202,4	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10047970	0.86[CEU][hapmap];0.86[TSI][hapmap]
rs10152754	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070693	0.83[MEX][hapmap]
rs11070696	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs11070697	0.85[ASN][1000 genomes]
rs11070708	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070713	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630629	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11632201	0.90[ASN][1000 genomes]
rs11632674	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs11634751	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11636378	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11857320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440323	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs12441304	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs12594670	0.86[ASN][1000 genomes]
rs12899680	0.86[ASN][1000 genomes]
rs12905627	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1395902	0.81[EUR][1000 genomes]
rs1507618	0.81[AFR][1000 genomes]
rs1532955	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1588130	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1605481	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1605484	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17482113	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1874615	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs1911614	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2413953	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2413954	0.86[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2413959	0.86[CEU][hapmap]
rs2601020	0.84[EUR][1000 genomes]
rs28562087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28788326	0.81[EUR][1000 genomes]
rs28842346	0.81[EUR][1000 genomes]
rs28871940	0.81[EUR][1000 genomes]
rs2899433	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2899448	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4303431	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs4350524	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs4775814	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4775815	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4775817	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56692783	0.81[EUR][1000 genomes]
rs62021586	0.81[EUR][1000 genomes]
rs62021587	0.81[EUR][1000 genomes]
rs6493371	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6493376	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs692008	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7161744	0.86[ASN][1000 genomes]
rs7162800	0.86[CHB][hapmap];0.87[MEX][hapmap]
rs7163740	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7164283	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166202	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs7166498	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7167041	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7167429	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs7169799	0.85[ASN][1000 genomes]
rs7170426	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs7176306	0.94[ASW][hapmap];0.91[LWK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs7178143	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs7178468	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs7181916	0.81[EUR][1000 genomes]
rs7182072	0.81[EUR][1000 genomes]
rs731051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733097	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs8027730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs8033476	0.89[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs8035468	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs8041493	0.81[EUR][1000 genomes]
rs925103	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs962710	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9635335	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs965134	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs9972329	0.86[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]

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	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1048348	DTWD1	cis	cerebellum	SCAN
rs1048348	CATSPER2P1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
2	chr15:49914400-49936400	Weak transcription	Small Intestine	intestine
3	chr15:49914400-49938000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:49914800-49937800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:49915000-49936600	Weak transcription	Pancreas	Pancrea
6	chr15:49915400-49937800	Weak transcription	Brain Anterior Caudate	brain
7	chr15:49916000-49936400	Weak transcription	Psoas Muscle	Psoas
8	chr15:49918000-49938600	Weak transcription	Right Ventricle	heart
9	chr15:49918000-49938800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:49918200-49936600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:49918200-49936600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:49918200-49937200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:49918200-49938000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:49918200-49938400	Weak transcription	HepG2	liver
15	chr15:49918200-49942200	Weak transcription	GM12878-XiMat	blood
16	chr15:49918400-49938000	Weak transcription	Colonic Mucosa	Colon
17	chr15:49918600-49938800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr15:49919800-49940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:49920000-49938200	Weak transcription	Brain Angular Gyrus	brain
20	chr15:49920000-49940400	Weak transcription	A549	lung
21	chr15:49920200-49936600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:49920800-49936400	Weak transcription	K562	blood
23	chr15:49920800-49937800	Weak transcription	NHEK	skin
24	chr15:49920800-49938000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:49920800-49940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:49921000-49937600	Weak transcription	HMEC	breast
27	chr15:49924000-49936400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:49925200-49936400	Weak transcription	NHLF	lung
29	chr15:49926000-49938000	Weak transcription	NH-A	brain
30	chr15:49927000-49940000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:49927600-49938800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:49927800-49936800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:49927800-49938600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:49928000-49936600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:49928000-49940200	Weak transcription	Fetal Intestine Small	intestine
36	chr15:49928200-49936400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr15:49928200-49936400	Weak transcription	Left Ventricle	heart
38	chr15:49928200-49936600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:49928200-49936800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:49928200-49937800	Weak transcription	Fetal Stomach	stomach
41	chr15:49928200-49938200	Weak transcription	Gastric	stomach
42	chr15:49928200-49939600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:49928200-49940400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:49928200-49940600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:49928200-49943000	Weak transcription	Lung	lung
46	chr15:49928400-49936400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:49928400-49936400	Weak transcription	Fetal Lung	lung
48	chr15:49928400-49936600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:49928400-49936600	Weak transcription	Dnd41	blood
50	chr15:49928400-49937400	Weak transcription	Fetal Kidney	kidney

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