Variant report

Variant	rs3825957
Chromosome Location	chr15:60643115-60643116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1033027	0.88[EUR][1000 genomes]
rs10851676	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10851678	0.84[ASN][1000 genomes]
rs10851679	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11071519	0.91[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11071521	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs11631793	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631850	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634259	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439973	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440492	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441980	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12708462	0.84[EUR][1000 genomes]
rs12898604	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899562	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12904910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1551349	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1567408	0.88[EUR][1000 genomes]
rs1967370	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2014953	0.88[EUR][1000 genomes]
rs2063322	0.88[EUR][1000 genomes]
rs2063324	0.88[EUR][1000 genomes]
rs2063325	0.87[EUR][1000 genomes]
rs2085037	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2123828	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2123833	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2136553	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136555	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2168013	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175187	0.88[EUR][1000 genomes]
rs2202920	0.88[EUR][1000 genomes]
rs2414667	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414668	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2414670	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3743269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485290	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4530072	0.88[ASN][1000 genomes]
rs4775257	0.87[EUR][1000 genomes]
rs7165592	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7167571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7170178	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7170421	0.90[ASN][1000 genomes]
rs7172784	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7178033	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7179548	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7180174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027359	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8029375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033896	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8037326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039867	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920432	0.81[EUR][1000 genomes]
rs9920513	0.86[ASN][1000 genomes]
rs9920684	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9920883	0.88[EUR][1000 genomes]
rs9972449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3825957	C2CD4A	cis	cerebellum	SCAN
rs3825957	C1orf74	trans	brain	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:60633000-60651400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:60634600-60651200	Genic enhancers	A549	lung
3	chr15:60635600-60650000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:60636000-60651800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:60636200-60643600	Strong transcription	HSMM	muscle
6	chr15:60636200-60646000	Weak transcription	Brain Substantia Nigra	brain
7	chr15:60636200-60646400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:60636400-60644200	Strong transcription	NH-A	brain
9	chr15:60636400-60648600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:60636600-60657800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:60637000-60648200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:60637000-60654800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:60637200-60649600	Strong transcription	Esophagus	oesophagus
14	chr15:60637200-60649800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr15:60637200-60652800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:60637200-60653600	Strong transcription	Placenta	Placenta
17	chr15:60637200-60654000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:60637200-60656800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:60637200-60656800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:60637400-60643400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:60637400-60645600	Strong transcription	HMEC	breast
22	chr15:60637400-60649600	Strong transcription	Colonic Mucosa	Colon
23	chr15:60637400-60658000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:60637600-60645600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:60637600-60647200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:60637600-60650200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:60637600-60651400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:60637600-60658000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr15:60637800-60645600	Strong transcription	Hela-S3	cervix
30	chr15:60637800-60647600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:60637800-60649400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:60637800-60649400	Strong transcription	Ovary	ovary
33	chr15:60637800-60649600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:60637800-60650000	Strong transcription	Fetal Intestine Small	intestine
35	chr15:60637800-60652400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:60638000-60646000	Weak transcription	Brain Angular Gyrus	brain
37	chr15:60638000-60654200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:60638000-60654600	Strong transcription	NHEK	skin
39	chr15:60638000-60655000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr15:60638200-60649600	Strong transcription	Colon Smooth Muscle	Colon
41	chr15:60638200-60649600	Strong transcription	Fetal Lung	lung
42	chr15:60638200-60650800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:60638200-60655000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:60638400-60644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:60638400-60649200	Strong transcription	Stomach Smooth Muscle	stomach
46	chr15:60638400-60651800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:60638400-60656800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr15:60638600-60648400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:60638600-60649800	Strong transcription	GM12878-XiMat	blood
50	chr15:60639000-60645600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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