Variant report

Variant	rs1044474
Chromosome Location	chr15:40845952-40845953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40845102..40847771-chr15:40879538..40882866,3	K562	blood:
2	chr15:40838014..40841452-chr15:40845857..40849279,3	MCF-7	breast:
3	chr15:40842151..40844272-chr15:40844325..40846704,2	K562	blood:
4	chr15:40837677..40839661-chr15:40843684..40846554,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10152546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10518697	0.96[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1058734	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070283	0.96[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs11630273	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633184	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637422	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12148915	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs12324748	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12385982	0.86[EUR][1000 genomes]
rs12592524	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12903817	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12908316	0.84[EUR][1000 genomes]
rs12913296	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913739	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12915171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915636	0.87[EUR][1000 genomes]
rs13329076	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970758	0.90[YRI][hapmap]
rs17673703	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[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];1.00[ASN][1000 genomes]
rs17674454	0.96[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17747423	0.87[EUR][1000 genomes]
rs17747633	0.96[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1801321	0.89[CEU][hapmap]
rs1814541	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2053973	0.95[YRI][hapmap]
rs2412525	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28634695	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647196	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669075	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824658	0.83[EUR][1000 genomes]
rs35127391	0.89[EUR][1000 genomes]
rs35684277	0.81[EUR][1000 genomes]
rs35842610	0.90[EUR][1000 genomes]
rs4923880	0.85[EUR][1000 genomes]
rs4924486	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4924496	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62019876	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62019879	0.90[EUR][1000 genomes]
rs71471880	0.81[EUR][1000 genomes]
rs7165509	0.96[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7170288	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175747	0.80[EUR][1000 genomes]
rs7177265	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs7180135	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8038122	0.81[EUR][1000 genomes]
rs957603	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs9920642	0.81[EUR][1000 genomes]
rs9920676	0.87[EUR][1000 genomes]
rs999197	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs1044474	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs1044474	CCDC32	cis	lesional skin	skin_eQTL
rs1044474	C15orf57	cis	Esophagus Muscularis	GTEx
rs1044474	C15orf57	cis	lung	GTEx
rs1044474	C15orf57	cis	Adipose Subcutaneous	GTEx
rs1044474	C15orf57	cis	Nerve Tibial	GTEx
rs1044474	MRPL42P5	cis	lymphoblastoid	seeQTL
rs1044474	C15orf57	cis	parietal	SCAN
rs1044474	C15orf57	cis	Esophagus Mucosa	GTEx
rs1044474	RAD51	cis	multi-tissue	Pritchard
rs1044474	C15orf57	cis	Artery Aorta	GTEx
rs1044474	CASC5	cis	cerebellum	SCAN
rs1044474	C15orf57	cis	Artery Tibial	GTEx
rs1044474	C15orf57	cis	cerebellum	SCAN
rs1044474	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs1044474	CCDC32	cis	multi-tissue	Pritchard
rs1044474	RP11-111A22.1	cis	lung	GTEx
rs1044474	C15orf57	cis	Muscle Skeletal	GTEx
rs1044474	RP11-111A22.1	cis	Artery Aorta	GTEx
rs1044474	CCDC32	cis	uninvolved skin	skin_eQTL
rs1044474	CCDC32	cis	normal skin	skin_eQTL
rs1044474	C15orf57	cis	Stomach	GTEx
rs1044474	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs1044474	C15orf57	cis	Heart Left Ventricle	GTEx
rs1044474	RP11-111A22.1	cis	Artery Tibial	GTEx
rs1044474	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs1044474	C15orf57	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40821400-40848000	Weak transcription	Brain Anterior Caudate	brain
2	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
4	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:40829800-40846000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:40831600-40856600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40838000-40848200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:40838000-40856400	Weak transcription	A549	lung
9	chr15:40838200-40846600	Strong transcription	Fetal Intestine Small	intestine
10	chr15:40838600-40847000	Weak transcription	Fetal Brain Male	brain
11	chr15:40838600-40852800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:40838600-40855600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:40838800-40846200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:40838800-40846600	Strong transcription	Fetal Stomach	stomach
15	chr15:40839000-40847200	Weak transcription	Brain Angular Gyrus	brain
16	chr15:40839200-40848600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:40839200-40849000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:40839200-40849000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:40839200-40849600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:40839200-40850000	Strong transcription	Fetal Thymus	thymus
21	chr15:40839400-40846600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:40839400-40847800	Weak transcription	HUVEC	blood vessel
23	chr15:40839400-40849600	Strong transcription	HMEC	breast
24	chr15:40839400-40850000	Strong transcription	Fetal Intestine Large	intestine
25	chr15:40839600-40847600	Weak transcription	NHDF-Ad	bronchial
26	chr15:40839600-40849800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:40839800-40848200	Weak transcription	HepG2	liver
28	chr15:40840000-40848000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:40840000-40856400	Weak transcription	Fetal Brain Female	brain
30	chr15:40840000-40856600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:40840400-40847600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:40840400-40850600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:40840600-40846000	Strong transcription	Hela-S3	cervix
34	chr15:40840600-40848800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:40841200-40847800	Weak transcription	NH-A	brain
36	chr15:40841600-40846200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:40841600-40846400	Strong transcription	Thymus	Thymus
38	chr15:40842000-40849800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:40842000-40849800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:40842000-40849800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:40842400-40847800	Weak transcription	Brain Substantia Nigra	brain
42	chr15:40842400-40849000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:40842400-40856200	Weak transcription	Colonic Mucosa	Colon
44	chr15:40842600-40849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:40843000-40848200	Weak transcription	Esophagus	oesophagus
46	chr15:40843200-40848200	Weak transcription	Brain Hippocampus Middle	brain
47	chr15:40843200-40848800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:40843200-40856400	Weak transcription	Fetal Heart	heart
49	chr15:40843400-40846400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:40843600-40846400	Strong transcription	Lung	lung

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